Index (Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

absolute() - Method in class Tuple3d: Convert each dimension's component into its absolute value.
AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
AbsoluteValue() - Constructor for class AbsoluteValue
accept(S, T) - Method in interface CheckedBiConsumer: Calls the function.
accept(S) - Method in interface CheckedConsumer: Like Consumer.accept(T) but throws an exception.
accept(int) - Method in interface CheckedIntConsumer: Like IntConsumer.accept(int) but throws an exception.
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in class AcceptIterationList
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in interface AcceptIterationPredicate: Whether a particular voxels fulfills the condition or not.
accept(int, int) - Method in interface Histogram.BinConsumer: Accepts a particular bin and corresponding count.
accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface AfterCondition
accept(ObjectMask) - Method in class AndCondition
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface BeforeCondition
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class DistanceCondition
accept(ObjectMask, ObjectMask, ObjectMask) - Method in class IncreaseFeatureCondition
accept(ObjectMask) - Method in class NeighborhoodCondition
accept(ObjectMask) - Method in interface UpdatableBeforeCondition
accept(ObjectMask) - Method in class WrapAsUpdatable
accept(ParsedFilePathBag) - Method in class AtLeastZSlices
accept(ParsedFilePathBag) - Method in class CheckParsedFilePathBag
accept(Point2i, int) - Method in interface OffsettedPointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface OffsettedScalarTwoDimensionalConsumer: Accepts a point
accept(Point2i) - Method in interface PointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface ScalarThreeDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int) - Method in interface ScalarTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
acceptableProbability(AnnealScheme) - Method in class AssignMode
acceptableProbability(AnnealScheme) - Method in class DirectAssignMode
acceptableProbability(AnnealScheme) - Method in class TransformationAssignMode
AcceptanceProbabilityCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
AcceptanceProbabilityCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class AcceptanceProbabilityCalculator
accepted() - Method in interface DualMarks: The accepted marks.
AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate: The condition is accepted if any one of a list of AcceptIterationPredicate fulfills the condition.
AcceptIterationList() - Constructor for class AcceptIterationList
AcceptIterationPredicate - Interface in org.anchoranalysis.image.voxel.object.morphological.predicate: A condition that must be fulfilled for a particular iteration of a morphological operation to be accepted.
acceptPathViaRegEx(Path, Pattern) - Static method in class MatchRegularExpression
acceptProposal(ToDoubleFunction<T>) - Method in class OptimizationStep
accepts(Class<?>) - Method in class AssignerMatchClass
accepts(Class<?>) - Method in interface InitializationParameterAssigner: Whether a particular type of initialization parameters is accepted?
AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale: Provides functions to provide access and creation to/from the object-mask representation of a generic type.
AccessObjectMaskSimple - Class in org.anchoranalysis.image.core.object.scale: Provides access to the simple-case of a list of ObjectMasks.
AccessObjectMaskSimple() - Constructor for class AccessObjectMaskSimple
AcquisitionDateReader - Class in org.anchoranalysis.io.bioformats.metadata: Reads the image acquisition-date.
activateDebugMode(String) - Method in class ExecutionArguments: Activates debug-mode.
add(NamedBean<?>) - Method in class Define: Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.
add(Double) - Method in class DoubleList
add(Double) - Method in class DoubleSet
add(Integer) - Method in class IntegerList
add(Integer) - Method in class IntegerSet
add(T) - Method in interface PrimitiveBeanCollection: Add an element to the collection.
add(String) - Method in class StringList
add(String) - Method in class StringSet
add(Color) - Method in class ColorList: Appends a Color to the list.
add(RGBColor) - Method in class ColorList: Like ColorList.add(Color) but adds a RGBColor.
add(int, RGBColor) - Method in class ColorList: Inserts a Color into the list, at a particular index.
add(String, T) - Method in class NameValueMap: Adds an element.
add(NameValue<T>) - Method in class NameValueMap: Adds an element.
add(String, StoreSupplier<T>) - Method in class EagerEvaluationStore
add(String, StoreSupplier<T>) - Method in class LazyEvaluationStore
add(String, StoreSupplier<T>) - Method in interface NamedProviderStore: Adds an element to the store.
add(StatefulMessageLogger) - Method in class MessageLoggerList
add(Class<? extends InputFromManager>) - Method in class InputTypesExpected
add(SubmittedJob) - Method in class ConcurrentJobMonitor
add(Feature<? extends T>) - Method in class FeatureList: Adds a feature to the current list.
add(LabelledResultsVector) - Method in interface FeatureCalculationResults: Adds a results-element to be written.
add(String) - Method in class FeatureNameList: Adds a feature-name.
add(String, int) - Method in class FeatureNameMapToIndex: Adds a new featureName and index
add(ResultsVector) - Method in class ResultsVectorList: Add a ResultsVector to the list in the final position.
add(CacheTransferSource<? extends FeatureInput>) - Method in class CacheTransferSourceCollection
add(String, Feature<T>) - Method in class NamedFeatureStore: Adds a named-feature to the store.
add(BoundingBox) - Method in class BoundingBoxesOnPlane
add(ObjectMask) - Method in class ObjectCollectionWithProperties: Add an ObjectMask to the collection, assigning empty properties to it.
add(ObjectWithProperties) - Method in class ObjectCollectionWithProperties: Add an ObjectWithProperties to the collection.
add(String, Stack) - Method in class NamedStacks: Add a stack.
add(String, StoreSupplier<Stack>) - Method in class NamedStacks
add(String, Stack) - Method in class NamedStacksUniformSize: Adds an element to the store.
add(RasterGenerator<T>) - Method in class CombineRasterGenerator
add(ChannelEntry) - Method in class NamedEntries
add(NamedChannelsForSeries) - Method in class NamedChannelsForSeriesConcatenate
add(Stack) - Method in class StackSeries
add(Stack) - Method in class TimeSequence
add(String, StoreSupplier<TimeSequence>) - Method in class WrapStackAsTimeSequenceStore
add(AcceptIterationPredicate) - Method in class AcceptIterationList: Adds an item to the list of predicates.
add(ObjectMask) - Method in class ObjectCollection: Adds an object to the collection.
add(VoxelStatistics) - Method in class VoxelStatisticsCombined: Adds an element.
add(String, Generator<T>) - Method in class CombinedListGenerator
add(FileType[]) - Method in class ConcatenateFileTypes
add(T) - Method in class OutputSequenceIncrementing: Outputs an additional element in the sequence.
add(T, S) - Method in class OutputSequenceIndexed: Outputs an additional element in the sequence.
add(T, Optional<S>) - Method in class OutputSequenceIndexed: Outputs an additional element in the sequence.
add(OutputtedFile) - Method in class RootDirectory
add(MutableDirectory) - Method in class RootDirectory
add(OutputtedFile) - Method in class Subdirectory
add(String, boolean) - Method in class RecordedOutputs: Adds a new output-name to the set of recorded names.
add(RunningSum) - Method in class RunningSum: Adds the values of another RunningSum to the current values.
add(double) - Method in class RunningSumExtrema: Adds a value to the running-sum, also remembering if value is the minimum or maximum of calls to this method.
add(double) - Method in class VarianceCalculatorDouble: Adds a value to the running sum.
add(int) - Method in class VarianceCalculatorLong: Adds a value to the running sum.
add(int, int) - Method in class VarianceCalculatorLong: Adds a multiple instances of a value to the running sum.
add(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
add(double) - Method in class EnergyTotal
add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
add(VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
add(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
add(EnergyTotal) - Method in class EnergySavedInd
add(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
add(String, EnergyScheme) - Method in class EnergySchemeSet
add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class EnergyMemoList
add(VoxelizedMarkMemo) - Method in class MemoList
add(UpdatableMarks) - Method in class UpdatableMarksList
add(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
add(MemoForIndex) - Method in class UpdatableMarksList
add(int, UpdatableMarks) - Method in class UpdatableMarksList
add(IndexByRegion<T>) - Method in class IndexByChannel
add(String, StoreSupplier<T>) - Method in interface MultiInputSubMap: Adds an entry to the map
add(String, StoreSupplier<T>) - Method in class OperationMap
add(String, StoreSupplier<TimeSequence>) - Method in class StackWithMap
add(Mark, Color) - Method in class ColoredMarks
add(Mark, RGBColor) - Method in class ColoredMarks
add(Mark) - Method in class MarkCollection
add(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
add(String) - Method in class ErrorNode
add(Exception) - Method in class ErrorNode
add(String) - Method in class ErrorNodeImpl
add(Exception) - Method in class ErrorNodeImpl
add(String) - Method in class ErrorNodeNull
add(Exception) - Method in class ErrorNodeNull
add(FeedbackReceiver<T>) - Method in class FeedbackReceiverList
add(TerminationCondition) - Method in class TerminationConditionListOr
add(AggregateReceiver<T>) - Method in class AggregateReceiverList
add(PeriodReceiver<T>) - Method in class PeriodReceiverList
add(WeightedKernel<T, S>) - Method in class WeightedKernelList
add(Overlay, RGBColor) - Method in class ColoredOverlayCollection
add(Overlay) - Method in class OverlayCollection
add(String, String) - Method in class OverlayProperties
add(String, int) - Method in class OverlayProperties
add(double) - Method in class AxisLimits
add(ImageCounter<T>) - Method in class ImageCounterList
add(LevelResult) - Method in class LevelResultCollection
add(CheckedSupplier<LabelledResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Method in class FeatureResultsAndThumbnails: Adds results, together with a thumbnail.
add(S, T) - Method in interface AddToAggregateItem
add(Optional<String>, String, S) - Method in class GroupMapByName: Adds an item with an identifier
add(T, String) - Method in class FileLabelMap
add(ImageMetadataInput) - Method in class ImageSize
add(ImageMetadataInput) - Method in class SummarizerImageMetadataSimple
add(T) - Method in class SummarizerInputFromManager
add(Path) - Method in class ExtensionCount
add(Path) - Method in class FilePathPattern
add(Path) - Method in class FileSizeStatistics
add(T) - Method in class Summarizer: Adds a element to the summary.
add(T) - Method in class SummarizerAggregate
add(T) - Method in class SummarizerCount
add(T) - Method in class SummarizerListMultiline
add(T) - Method in class SummarizerSplitMoreThan
add(FileDetails) - Method in class ParsedFilePathBag
add(int, String) - Method in class SortedSetChannel
add(Point3i) - Method in class PointRange: Adds a new point to be considered in the range.
add(int, int, int) - Method in class PointRange: Adds a new point to be considered in the range.
add(Point2i) - Method in class Point2d: Arithmetically adds a Point2i's values across each dimension.
add(Point2d) - Method in class Point2d: Arithmetically adds a Point2d's values across each dimension.
add(Point2i) - Method in class Point2i: Adds values from a Point2i across each corresponding dimension.
add(double, double, double) - Method in class Tuple3d: Arithmetically adds values to each dimension's component.
add(Tuple3d) - Method in class Tuple3d: Arithmetically adds a Tuple3d's values across each dimension.
add(ReadableTuple3i) - Method in class Tuple3d: Arithmetically adds a ReadableTuple3i's values across each dimension.
add(ReadableTuple3i) - Method in class Tuple3i: Arithmetically adds a ReadableTuple3i's values across each dimension.
add(BoundingBox, T) - Method in class BoundingBoxRTree: Adds a bounding-box with a corresponding payload.
add(double, double, T) - Method in class IntervalRTree: Adds a bounding-box with a corresponding index.
add(Rectangle, T) - Method in class RTree: Adds a Rectangle with a corresponding payload.
addAdditionalOptions(Options) - Method in class LauncherConfig
addAdditionalOptions(Options) - Static method in class CommandLineOptions
addAll(Define) - Method in class Define: Adds all the named-beans from source to the current map.
addAll(List<NamedBean<T>>) - Method in class Define: Adds all the named-beans from source to the current map.
addAll(ColorList) - Method in class ColorList: Appends Colors to the list.
addAll(FeatureList<? extends T>) - Method in class FeatureList: Add all the features in other to the current list.
addAll(ObjectCollection) - Method in class ObjectCollection: Adds all objects in objects to the collection.
addAll(Collection<? extends ObjectMask>) - Method in class ObjectCollection: Adds all objects in collection to the collection.
addAll(MemoForIndex) - Method in class MemoList
addAll(Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
addAll(int, Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
addAll(MarkCollection, RGBColor) - Method in class ColoredMarks
addAll(ColoredMarks) - Method in class ColoredMarks
addAll(MarkCollection) - Method in class MarkCollection
addAll(OverlayCollection) - Method in class OverlayCollection
addAll(Collection<S>) - Method in class ImageCounterList
addAll(Collection<T>) - Method in class Summarizer: Adds the elements to the summary.
addAllOutputNamesTo(OutputEnabledMutable) - Method in class DefineOutputter: Adds all possible output-names to a OutputEnabledMutable.
addAllToUpdatablePairList(UpdatableMarksList) - Method in class VoxelizedMarksWithEnergy
addAnnotatedImage(T) - Method in interface ImageCounter: Add an image that had an associated annotation.
addAnnotatedImage(T) - Method in class ImageCounterList
addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in interface NamedChannelsForSeries
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in interface NamedChannelsForSeries
addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in class NamedChannelsForSeriesConcatenate
addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in class NamedChannelsForSeriesMap
addAssignedPair(ObjectMask, ObjectMask, double) - Method in class OverlappingObjects: Adds an assigned pair of objects with a particular overlap-ratio.
addBasicOptions(Options) - Static method in class CommandLineOptions
addBlankChannel() - Method in class Stack: Adds a new empty Channel in the final-most position in the list.
addChangeID(Mark, Color) - Method in class ColoredMarks
addChangeID(Mark, RGBColor) - Method in class ColoredMarks
addChannel(Channel) - Method in class Stack: Appends a channel to the stack, as the new final-most channel position-wise.
addChannel(Channel) - Method in class StackNotUniformSized: Appends a channel to the stack, as the new final-most channel positionwise.
addChannelsFrom(Stack) - Method in class Stack: Add the channels from another instance into this instance.
AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
AddConstant() - Constructor for class AddConstant
AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
AddConstantTo() - Constructor for class AddConstantTo
AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: Add Criteria
AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class AddCriteriaEnergyPair
AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
AddCriteriaFeatureRelationThreshold() - Constructor for class AddCriteriaFeatureRelationThreshold
AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaNever() - Constructor for class AddCriteriaNever
AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaOr() - Constructor for class AddCriteriaOr
AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaPair() - Constructor for class AddCriteriaPair
addDefaultOutputs(OutputEnabledMutable) - Method in class AnnotationComparisonAssigner: Adds any default outputs that should occur from the assigner.
addDefaultOutputs(OutputEnabledMutable) - Method in class FeatureCostAssigner
addDefaultOutputs(OutputEnabledMutable) - Method in class MaskIntersectionAssigner
addDictionary(String, Dictionary) - Method in class ImageInitialization: Adds a dictionary to named-collection of dictionaries.
AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define: Performs a Watershed on distance transform by bundling together several other beans.
AddDistanceTransform() - Constructor for class AddDistanceTransform
addDouble(String, double) - Method in class StatisticsToExport: Adds a statistic that is a double.
addDoubleAsString(String, double) - Method in class OverlayProperties
AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
AddDualTransformer() - Constructor for class AddDualTransformer
addEdge(V, V) - Method in class GraphWithoutPayload: Add an edge between two vertices.
addEdge(V, V, P) - Method in class GraphWithPayload: Add an edge between two vertices.
AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
AddEdgeFilters() - Constructor for class AddEdgeFilters
addEdges(V, Collection<V>) - Method in class GraphWithoutPayload: Adds edge(s) from the vertex from to each element in toCollection.
addEnabledOutputFirst(String...) - Method in class OutputEnabledMutable: Adds enabled first-level outputs.
addEnabledOutputs(OutputEnabledMutable) - Method in class OutputEnabledMutable: Adds enabled outputs from another OutputEnabledMutable.
addEnabledOutputSecond(String, String...) - Method in class OutputEnabledMutable: Adds enabled second-level outputs.
AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
AddEnergy() - Constructor for class AddEnergy
addErrorDescription(StringBuilder) - Method in class ErrorNode
addErrorDescription(StringBuilder) - Method in class ErrorNodeImpl
addErrorDescription(StringBuilder) - Method in class ErrorNodeNull
addErrorLevel(String) - Method in class ProposerContext
addFormatted(String, Object...) - Method in class ErrorNode
addFormatted(String, Object...) - Method in class ErrorNodeImpl
addFormatted(String, Object...) - Method in class ErrorNodeNull
addForSlice(int, int) - Method in interface VoxelPartition
addForSlice(int, int) - Method in class VoxelPartitionHistogram
addFrom(BeanInstanceMap) - Method in class BeanInstanceMap: Populates the entries from another BeanInstanceMap
addFrom(List<NamedBean<?>>) - Method in class BeanInstanceMap: Populates from a list of NamedBean.
addFrom(NamedProvider<Stack>) - Method in class NamedStacks: Adds a Stack from a NamedProvider.
addFrom(CommandLineExtracter, InputArguments) - Static method in class AddInputOptions: Adds options to change the inputs from the command-line.
addFrom(CommandLineExtracter, OutputArguments) - Static method in class AddOutputOptions: Adds options to add/remove change the outputs the inputs from the command-line.
addFromList(FeatureList<FeatureInput>) - Method in class SharedFeatures: Add features from a feature-list.
addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class SharedFeatures: Add features from a NamedProvider of feature-lists.
addFromWithPrefix(NamedProvider<Stack>, String) - Method in class NamedStacks: Like NamedStacks.addFrom(NamedProvider) but additionally adds a prefix to the name when adding.
addFromXmlFile(Path) - Method in class RootPathMap: Adds root-paths contained in a list of XML Beans in an xml file
addHistogram(Histogram) - Method in class Histogram: Adds the counts from another histogram to the current object.
addIgnoreInfinity(double) - Method in class AxisLimits
addInputOptions(Options) - Static method in class CommandLineOptions
AddInputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to inputting from the command-line.
addInt(String, int) - Method in class StatisticsToExport: Adds a statistic that is an int.
additionalLabelsFor(FileInput) - Method in class FromHistogram
additionalLabelsFor(ProvidesStackInput) - Method in class FromImage
additionalLabelsFor(ImageMetadataInput) - Method in class FromImageMetadata
additionalLabelsFor(T) - Method in class SingleRowPerInput: Additional labels for an input to include (after the identifier, and before any group labels).
addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class BarPlot
addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class BoxPlot
addLabelToDataset(S, T, int, String, String) - Method in class PlotIndexBaseCategorical
addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
addMeanExtrema(String, double, double, double) - Method in class StatisticsToExport: Adds three statistics a mean, min and max.
addMeanExtrema(String, RunningSumExtrema) - Method in class StatisticsToExport: Like StatisticsToExport.addMeanExtrema(String, double, double, double) but determines the statistics from a RunningSumExtrema.
addMultiple(RGBColor, int) - Method in class ColorList: Append multiple entries for the same color to the end of the list.
addObjectsNoBoundingBoxChange(Collection<T>) - Method in class BoundedList: Adds elements without changing the bounding-box
addObjectsToGraph(ObjectCollection) - Method in class MergeGraph
addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class ColoredObjectCollection: Adds objects from a ObjectCollectionProvider all with one specific color
addOperationRecorder(WriteOperationRecorder) - Method in class Outputter
addOperationRecorder(WriteOperationRecorder) - Method in class OutputterChecked: Adds an additional operation recorder alongside any existing recorders.
addOptionsFromCommandLine() - Method in class AddInputOptions
AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process: Base class for adding options from command-line arguments.
AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class AddOptionsFromCommandLine
addOptionsFromCommandLine() - Method in class AddOptionsFromCommandLine: Maybe add options to the arguments from the command-line.
addOptionsFromCommandLine() - Method in class AddOutputOptions
AddOutputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to outputting from the command-line.
addResultsFor(LabelledResultsVector) - Method in class GroupedResults: Adds a result to the group-writer, but doesn't write yet.
addRow(LabelledResultsVector) - Method in class FeatureCSVWriter: Directly adds a row of feature-values.
addRow(List<TypedValue>) - Method in class FeatureCSVWriter: Directly adds a row in the form of typed-values.
addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class ImageInitialization
addShift(ReadableTuple3i) - Method in class ContiguousVoxelPath: Adds a shift to each point (modifying the existing points in memory), and returns them as a list
addSlice(VoxelBuffer<T>) - Method in interface ProjectableBuffer: Adds a slice to the buffer.
addStack(Provider<Stack>) - Method in class ArrangeRaster: Adds a stack to the existing list of stack-providers.
addString(String, String) - Method in class StatisticsToExport: Adds a statistic that is a String.
addTimestamp(long) - Method in class ClusterIdentifier: Adds a timestamp to the cluster.
addTo(Define) - Method in class Concatenate
addTo(Define) - Method in interface DefineAdder: Adds items to define.
addTo(Define) - Method in class FromXMLList
addTo(ObjectMask, int) - Method in interface VoxelsArithmetic: Adds a constant-value to each voxel but only for voxels inside an object-mask.
addTo(Define) - Method in class AddDistanceTransform
addTo(S, T) - Method in class GroupMapByName
addTo(Define) - Method in class AddEdgeFilters
addTo(Define) - Method in class VisualizeOnBackground
AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped: Adds an individual-item to an aggregate-item
AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules: Adds additional outputs-names to be enabled to the defaults.
AddToDefaults() - Constructor for class AddToDefaults
addToErrorNode(ErrorNode) - Method in exception ErrorNodeException
addToManager(MultiInputManager, String, String) - Method in class FilePathBaseAppendToManager
addToRow(List<TypedValue>) - Method in class RowLabels: Adds the identifiers to a row to be outputted in a features CSV.
addToStacks(String, Stack) - Method in class ImageInitialization
addToStacks(String, StackProvider) - Method in class ImageInitialization
addToStore(NamedProviderStore<T>, Logger) - Method in interface MultiInputSubMap: Copies all the existing entries into a NamedProviderStore.
addToStore(NamedProviderStore<T>, Logger) - Method in class OperationMap
addToStore(NamedProviderStore<TimeSequence>, Logger) - Method in class StackWithMap
addToStore(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class StackWithMap
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class NamedChannelsInput
addToStoreInferNames(NamedProviderStore<Stack>, Logger) - Method in interface ProvidesStackInput: Adds the current object to a named-store of stacks (using the default series).
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in interface ProvidesStackInput: Adds the current object to a named-store of stacks.
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class MultiInput
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class ConvertNamedChannelsInputToStack
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class NamedChannelsInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in interface ProvidesStackInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class MultiInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class ConvertNamedChannelsInputToStack
addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
addToVoxelList(int, int, int) - Method in class IndexByRegion
addTypedValuesTo(Collection<TypedValue>, int) - Method in class ResultsVector: Adds TypedValue representations of the results to a Collection.
addUnannotatedImage() - Method in interface ImageCounter: Add an image that did not have an associated annotation.
addUnannotatedImage() - Method in class ImageCounterList
addUnassignedLeft(ObjectMask) - Method in class OverlappingObjects: Add an unassigned object to the left set.
addUnassignedLeft(ObjectCollection) - Method in class OverlappingObjects: Add unassigned objects to the left set.
addUnassignedRight(ObjectMask) - Method in class OverlappingObjects: Add an unassigned object to the right set.
addUnassignedRight(ObjectCollection) - Method in class OverlappingObjects: Add unassigned objects to the right set.
addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition: Adds job-manifests that don't have corresponding experiment-manifests.
addUnused(T) - Method in interface VoxelPartitionFactory
addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
addVertex(V) - Method in class GraphWithoutPayload: Adds a vertex.
addVertex(V) - Method in class GraphWithPayload: Adds a vertex.
addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOption
addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionDual
addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionSingle
addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean: Add an item to define with a name being added.
addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class OverlayProperties
AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
AdjacentFile() - Constructor for class AdjacentFile
adjacentVerticesOutgoing(V) - Method in class GraphWithoutPayload: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoing(V) - Method in class GraphWithPayload: The vertices that are connected to a particular vertex by an outgoing edge.
adjacentVerticesOutgoingStream(V) - Method in class GraphWithoutPayload: Like GraphWithoutPayload.adjacentVerticesOutgoing(V) but returns a Stream instead of a Set.
adjacentVerticesOutgoingStream(V) - Method in class GraphWithPayload: Like GraphWithPayload.adjacentVerticesOutgoing(V) but returns a Stream instead of a Set.
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task: Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
afterAllJobsAreExecuted(ComparisonSharedState<T>, InputOutputContext) - Method in class CompareAnnotations
afterAllJobsAreExecuted(FeatureExporter<S>, InputOutputContext) - Method in class ExportFeatures
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ConvertImageFormat
afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase
afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class ImageAssignLabel
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ScaleImage
afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class SegmentInstanceWithModel
afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class ExtractSlice
afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class MovieFromSlices
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class CombineCSV
afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class CopyFiles
afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class SummarizeBase
afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class ConvertNamedChannels
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportReportFeaturesFromManifest
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class ExportReportFeaturesFromMulti
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportObjectsAsCroppedImages
afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class ExportObjectsFromCSV
afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class SegmentMarksFromImage
AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitScheduler
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerAnd
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerConvexAboutRoot
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerMaxDistanceAlongContour
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerUniformSample
aggEnd(Aggregator) - Method in interface AggregateReceiver
aggEnd(Aggregator) - Method in class AggregateReceiverList
aggEnd(Aggregator) - Method in class ConsoleAggregatedReporter
aggEnd(Aggregator) - Method in class CSVReporterAggregated
aggEnd(Aggregator) - Method in class Log4JReporter
aggEnd(Aggregator) - Method in class OptimizationStepLogReporter
aggEnd(Aggregator) - Method in class TextFile
AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggIDCounter(int) - Constructor for class AggIDCounter
AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate: Aggregates many per-image annotations together in form of a CSV file.
AggregateAnnotations() - Constructor for class AggregateAnnotations
AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateReceiverList() - Constructor for class AggregateReceiverList
aggregateResults(List<Double>) - Method in class FeatureIntersectingObjectsSingleElement
aggregateResults(List<Double>) - Method in class MaxFeatureIntersectingObjects
aggregateResults(List<Double>) - Method in class MinFeatureIntersectingObjectsAboveThreshold
aggregateResults(List<Double>) - Method in class NumberIntersectingObjectsAboveThreshold
AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class AggregateTriggerBank
Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
Aggregator(int) - Constructor for class Aggregator
AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregatorException() - Constructor for exception AggregatorException
AggregatorException(String) - Constructor for exception AggregatorException
AggregatorException(Exception) - Constructor for exception AggregatorException
aggReport(Reporting<T>, Aggregator) - Method in interface AggregateReceiver
aggReport(Reporting<T>, Aggregator) - Method in class AggregateReceiverList
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface AggregateReceiver
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class AggregateReceiverList
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
All - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed irrespective of outputName.
All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects all possible channels from all possible stacks
All() - Constructor for class All
allAssociatedPaths() - Method in interface InputFromManager: A path to all files associated with the input, including InputFromManager.pathForBinding().
allChannelsAsStack(int, Logger) - Method in interface NamedChannelsForSeries
allChannelsAsStack(int, Logger) - Method in class NamedChannelsForSeriesConcatenate
allChannelsAsStack(int, Logger) - Method in class NamedChannelsForSeriesMap
allChannelsEightBit() - Method in class StackWriteAttributes: Mark the attributes to indicate that channels are no longer guaranteed to be 8-bit.
allChannelsHaveIdenticalType() - Method in class Stack: Determines if all channels have an identical voxel data-type.
allChannelsHaveType(VoxelDataType) - Method in class RGBStack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class Stack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class TimeSequence
allExtensions() - Method in enum ImageFileFormat: All extensions associated with a file-format.
allFileTypes() - Method in class ConcatenateFileTypes
allHeaders() - Method in class LabelHeaders: The non-group and group headers combined (in this order respectively)
allImageExtensions() - Static method in class FormatExtensions: The extensions of all image file formats as enumerated in ImageFileFormat.
allLabels(NoSharedState) - Method in class BinaryOutcomeImageLabeller
allLabels(ImageCSVLabellerInitialization) - Method in class ImageCSVLabeller
allLabels(T) - Method in class ImageLabeller: A set of identifiers for all groups that can be outputted by the labeller.
allLabels(ImageLabellerStringMapInitialization<T>) - Method in class ImageLabellerStringMap
allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class IterateVoxelsObjectMask: Do all points on an object-mask match a predicate on the point's voxel-intensity?
allocate(int) - Static method in class UnsignedByteBuffer: Allocates a new buffer of unsigned-bytes.
allocate(int) - Static method in class UnsignedIntBuffer: Allocates a new (direct) buffer of unsigned-ints.
allocate(int) - Static method in class UnsignedShortBuffer: Allocates a new (direct) buffer of unsigned-shorts.
allocateFloat(int) - Static method in class VoxelBufferFactory: Allocates a new float voxel-buffers of given size.
allocateFloatArray(int) - Static method in class VoxelBufferFactory: Creates an array of float voxel-buffers of given size.
allocateUnsignedByte(int) - Static method in class VoxelBufferFactory: Allocates a new unsigned byte voxel-buffer of given size.
allocateUnsignedByteArray(int) - Static method in class VoxelBufferFactory: Creates an array of unsigned byte voxel-buffers of given size.
allocateUnsignedInt(int) - Static method in class VoxelBufferFactory: Allocates a new unsigned int voxel-buffers of given size.
allocateUnsignedIntArray(int) - Static method in class VoxelBufferFactory: Creates an array of unsigned int voxel-buffers of given size.
allocateUnsignedShort(int) - Static method in class VoxelBufferFactory: Allocates a new unsigned short voxel-buffers of given size.
allocateUnsignedShortArray(int) - Static method in class VoxelBufferFactory: Creates an array of unsigned short voxel-buffers of given size.
AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region: Only considers voxels with non-zero intensity.
AllSlicesMaskEverythingNonZero() - Constructor for class AllSlicesMaskEverythingNonZero
AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region: Gets all slices where indexNonZero has at least one non-zero pixel in that slice
AllSlicesMaskNonZero() - Constructor for class AllSlicesMaskNonZero
allSuccessful() - Method in class TaskStatistics: Did all jobs execute and completely successfully?
AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Creates a new mask of particular dimensionality where all values are off.
AllValuesOff() - Constructor for class AllValuesOff
AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Creates a new mask of particular dimensionality where all values are on.
AllValuesOn() - Constructor for class AllValuesOn
ALPHA - Static variable in class RGBChannelNames: Name for the alpha channel.
Always - Class in org.anchoranalysis.plugin.image.bean.object.match: Specifies a single object that will always be the "match" for whatever source object.
Always() - Constructor for class Always
always2D(String) - Static method in class OutputSequenceStackFactory: The stacks that are outputted are guaranteed to be two-dimensional.
always2D(boolean) - Method in class StackWriteAttributes: Derives a StackWriteAttributes that will always be 2D, but is otherwise unchanged.
AlwaysAllowed - Class in org.anchoranalysis.io.output.writer: Allows every output, irrespective of whether the OutputterChecked allows the output-name.
AlwaysAllowed(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class AlwaysAllowed
alwaysExecuteBeforeCallingLibrary() - Static method in class CVInit: This routine must always be executed at least once before calling any routines in the OpenCV library
AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace: Always create a new session-input with no reuse or caching.
AlwaysNew(CacheCreator) - Constructor for class AlwaysNew: Constructor with default means of creating a session-input
AlwaysNew(CacheCreator, ChildCacheFinder) - Constructor for class AlwaysNew
AlwaysReject - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: A special ImageMetadataReader that will always throw an exception and reject a file.
AlwaysReject() - Constructor for class AlwaysReject
AnchorBean<F> - Class in org.anchoranalysis.bean: The base class of all beans used in Anchor.
AnchorBean() - Constructor for class AnchorBean
AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory: Base class for all Anchor-specific bean factories.
AnchorBeanFactory() - Constructor for class AnchorBeanFactory
AnchorCheckedException - Exception in org.anchoranalysis.core.exception: A base class for all checked exceptions used on the Anchor platform.
AnchorCheckedException() - Constructor for exception AnchorCheckedException: Creates without message or cause.
AnchorCheckedException(String, Throwable) - Constructor for exception AnchorCheckedException: Creates with message and cause.
AnchorCheckedException(String) - Constructor for exception AnchorCheckedException: Creates with only a message.
AnchorCheckedException(Throwable) - Constructor for exception AnchorCheckedException: Creates with only a cause.
AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable: An exception that can be combined with similar exceptions and summarized.
AnchorCombinableException(String, Throwable) - Constructor for exception AnchorCombinableException: Creates with a description and a cause.
AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory: The default bean factory used for initializing AnchorBeans.
AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class AnchorDefaultBeanFactory
AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly: A base class for particular checked-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception AnchorFriendlyCheckedException: A user-friendly error message and its cause.
AnchorFriendlyCheckedException(String) - Constructor for exception AnchorFriendlyCheckedException: A user-friendly error message WITHOUT a cause.
AnchorFriendlyCheckedException(Throwable) - Constructor for exception AnchorFriendlyCheckedException: A wrapped exception.
AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly: A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception AnchorFriendlyRuntimeException: A user-friendly error message and its cause.
AnchorFriendlyRuntimeException(String) - Constructor for exception AnchorFriendlyRuntimeException: A user-friendly error message without a cause.
AnchorFriendlyRuntimeException(Throwable) - Constructor for exception AnchorFriendlyRuntimeException: A wrapped exception.
AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly: A run-time exception to throw in situations which should never logically occur by design.
AnchorImpossibleSituationException() - Constructor for exception AnchorImpossibleSituationException: Default constructor.
AnchorImpossibleSituationException(String) - Constructor for exception AnchorImpossibleSituationException: Creates with a specific message explaining the exception.
AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception: This is an exceotion that should never be thrown, but can be used for type-safety where an exception is needed
AnchorNeverOccursException() - Constructor for exception AnchorNeverOccursException
AnchorRuntimeException - Exception in org.anchoranalysis.core.exception: A base class for all unchecked (runtime) exceptions used on the Anchor platform.
AnchorRuntimeException() - Constructor for exception AnchorRuntimeException: Creates without message or cause.
AnchorRuntimeException(String, Throwable) - Constructor for exception AnchorRuntimeException: Creates with message and cause.
AnchorRuntimeException(String) - Constructor for exception AnchorRuntimeException: Creates with only a message.
AnchorRuntimeException(Throwable) - Constructor for exception AnchorRuntimeException: Creates with only a cause.
AnchorWebsiteLinks - Class in org.anchoranalysis.launcher: A centralized location for hyperlinks to the Anchor website.
and(StackWriteAttributes) - Method in class StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical and on each field.
And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
And() - Constructor for class And
And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical AND i.e.
And() - Constructor for class And
AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: Combines two UpdatableBeforeConditions as LOGICAL ANDs
AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class AndCondition
AndKernel - Class in org.anchoranalysis.image.voxel.kernel: Combines two BinaryKernels so that they only a true value exists only at a point where both kernels return true.
AndKernel(BinaryKernel, BinaryKernel) - Constructor for class AndKernel: Create for the two kernels.
AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
AndList() - Constructor for class AndList
AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
AndObjectsWithMasks() - Constructor for class AndObjectsWithMasks
AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider: Performs Perona-Malik Anisotropic Diffusion.
AnisotropicDiffusion() - Constructor for class AnisotropicDiffusion
AnnealScheme - Class in org.anchoranalysis.mpp.bean: Base class for approaches to simulated annealing.
AnnealScheme() - Constructor for class AnnealScheme
Annotation - Interface in org.anchoranalysis.annotation: Base class for types of image annotations.
AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
AnnotationAggregateCSVGenerator() - Constructor for class AnnotationAggregateCSVGenerator
AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean: How to display one or more Stacks as background during an annotation process.
AnnotationBackground() - Constructor for class AnnotationBackground
AnnotationComparisonAssigner<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Compares elements in an annotation to elements from an experiment.
AnnotationComparisonAssigner() - Constructor for class AnnotationComparisonAssigner
AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
AnnotationComparisonInput(T, Tuple2<ComparableSource, ComparableSource>, Tuple2<String, String>, StackReader) - Constructor for class AnnotationComparisonInput
AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
AnnotationComparisonInputManager() - Constructor for class AnnotationComparisonInputManager
AnnotationDeleter - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be deleted from the file-system.
annotationExistsAt(Path) - Method in class DualMarksAnnotationReader: Whether an annotation exists at a particular path on the file-system.
AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean: An InputManager that provides annotations corresponding to images.
AnnotationInputManager() - Constructor for class AnnotationInputManager
AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
AnnotationLabel() - Constructor for class AnnotationLabel
annotationLabelFor(ProvidesStackInput, Logger) - Method in class AnnotatorStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
annotationLabelFor(ProvidesStackInput, Logger) - Method in class ImageLabelStrategy
annotationLabelFor(ProvidesStackInput, Logger) - Method in class MarkProposerStrategy
AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be read from the file-system.
AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark: An image-annotation that involves a mark-collection.
AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io: One particular annotation, associated with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class AnnotationWithStrategy: Creates for a particular input and associated annotation strategy.
AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be written to the file-system.
AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean: How an input is associated with annotations on the file-system, and how this is presented visually.
AnnotatorStrategy() - Constructor for class AnnotatorStrategy
Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files to a number 001, 002 etc.
Anonymize() - Constructor for class Anonymize
AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class AnonymizeSharedState
any() - Method in class VoxelsUntyped: Exposes without any specific buffer type.
anyDimensionIsLargerThan(Extent) - Method in class Extent: Returns true if any dimension in this extent is larger than the corresponding dimension in other extent.
anyExists() - Method in class PredicateAtCorner
anyExists() - Method in class PredicateImplementation
anyExists() - Method in interface VoxelsPredicate: Does at least one value satisfy the predicate - across all voxels?
anyMatch(Predicate<ObjectMask>) - Method in class ObjectMaskStream: Does the predicate evaluate to true on any object in the collection?
anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class IterateVoxelsAll: Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check: The center ps of at least one slice should be on the stack Tries overall center point first, and then projects it onto each slice
AnySliceCenterOnMask() - Constructor for class AnySliceCenterOnMask
append(StatisticsToExport) - Method in class StatisticsToExport: Appends the names and values from another AnnotationComparison to the existing.
append(Optional<FeatureList<T>>) - Method in class FeatureList: Appends the features one or more (optional) feature-lists to the existing list.
AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A CSV that is appended from the root of a project
AppendCsv() - Constructor for class AppendCsv
AppendDictionary - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendDictionary() - Constructor for class AppendDictionary
appendExtension(String, Optional<String>) - Static method in class ExtensionUtilities: Appends an (optional) extension to a string, adding in the leading period if the extension is defined.
appendExtension(Path, Optional<String>) - Static method in class ExtensionUtilities: Like ExtensionUtilities.appendExtension(String, Optional) but accepts and returns a Path.
AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendFilePath() - Constructor for class AppendFilePath
AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendHistogram() - Constructor for class AppendHistogram
AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendMarks() - Constructor for class AppendMarks
AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendObjects() - Constructor for class AppendObjects
AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStack() - Constructor for class AppendStack
AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStackDirect() - Constructor for class AppendStackDirect
apply(Throwable, Writer, String, int, boolean) - Static method in class RecursivelyDescribeExceptionStack: Incrementally adds a line to a string builder with the message of each exception moving onto the next nested exception until there are no more
apply(S, T) - Method in interface CheckedBiFunction: Calls the function.
apply(S) - Method in interface CheckedFunction: Calls the function.
apply(int) - Method in interface CheckedIntFunction: Calls the function
apply(T) - Method in interface CheckedUnaryOperator: Applies the operation.
apply(int, int) - Method in interface IntBinaryOperation: Applies the operation on two integer values.
apply(ImageInitialization) - Static method in class CreateCombinedStack
apply(Mask, Mask) - Static method in class MaskAnd: Performs a logical and operation on each voxel in two masks, writing the result onto the second mask.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class MaskAnd: Performs a logical and operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(Mask, Mask) - Static method in class MaskOr: Performs a logical or operation on each voxel in two masks, writing the result onto the first mask.
apply(Mask, Mask) - Static method in class MaskXor: Performs a logical xor (exclusive or) operation on each voxel in two masks, writing the result onto the first mask.
apply(BinaryVoxels<UnsignedByteBuffer>, BinaryVoxels<UnsignedByteBuffer>) - Static method in class MaskXor: Performs a logical xor (exclusive or) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(List<ChannelEntry>) - Method in class NamedEntriesCreator
apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel: Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
apply(IFormatReader, ReadOptions, int) - Method in class DimensionsCreator
apply(String, Path) - Static method in class WriteStringToFile
applyAsDouble(T, U) - Method in interface CheckedToDoubleBiFunction: Applies this function to the given arguments.
applyAsFloat(int) - Method in interface IntToFloatFunction: Applies this function to the given argument.
applyAsInt(S) - Method in interface CheckedToIntFunction: Calls the function
applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class LinearLeastSquaresViaNormalEquationBase
applyDelta(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta: Applies the changes to enable or disable additional outputs, if they are defined.
applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class FitResult
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel: Applies the kernel to voxels and sums the returned value.
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel: Applies the kernel to voxels and sums the returned value.
applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel: Applies a BinaryKernel to voxels and counts how many true values occur en aggregate.
ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask: Applies an ImageJ (2D) morphological operation to voxels
applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class BeanInitializer: Applies the initialization to a bean if possible.
ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel: Applies various kinds of Kernel to BinaryVoxels.
applyMorphologicalOperation(Mask, boolean) - Method in class Dilate
applyMorphologicalOperation(Mask, boolean) - Method in class Erode
applyMorphologicalOperation(Mask, boolean) - Method in class MorphologicalOperatorBase
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Dilate
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Erode
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class ObjectCollectionProviderMorphological
applyOperation(UnaryOperator<Stack>, Optional<Dimensions>) - Method in class NamedStacks: Applies an operation on each Stack in the collection and returns a new derived collection.
applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateIncrementalOperationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateDilationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateErosionMap
applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class ApplyImageJMorphologicalOperation
applyRadiiSubtractScale(double, double) - Method in class FitResult
applyRankFilter(Channel, int, int) - Static method in class FilterHelper: Applies a 2D rank-filter to each slice independently.
applyStrategy(MergeCandidate) - Method in class MergeStrategy
applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel: Applies the kernel to voxels until a positive value is returned, then exits with true.
arbitraryElement() - Method in class RTree: Any arbitrary element from the tree.
ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Calculates deterministicly a point that is definitely inside the object-mask.
ArbitraryInsidePoint(String) - Constructor for class ArbitraryInsidePoint
ArbitraryInsidePoint() - Constructor for class ArbitraryInsidePoint
ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria: If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
ArbitraryPointCommon() - Constructor for class ArbitraryPointCommon
Area<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Area of the stack (XY dimensions only, Z dimension is not considered).
Area() - Constructor for class Area
areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class PointsNeighborChecker: Are all points in a list neighboring the next point in the list?
AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed in physical coordinates
AreaPhysical() - Constructor for class AreaPhysical
AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed as square pixels
AreaPixels(double) - Constructor for class AreaPixels
AreaPixels() - Constructor for class AreaPixels
areaXY() - Method in class Dimensions: Size in X multiplied by size in Y.
areaXY() - Method in class Extent: Size in X multiplied by size in Y.
areDocumentsEqual(Document, Document) - Static method in class CompareXML: Are two XML-documents equal in content, ignoring whitespace and comments?
areEqual(double, double) - Static method in class DoubleUtilities: Are the two numbers equal?
areEqual(float, float) - Static method in class FloatUtilities: Are the two numbers equal?
arePointsNeighbors(Point3i, Point3i) - Static method in class PointsNeighborChecker: Do two points have a big neighbor relationship to each other?
ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: Converts string passed as arguments.
arithmetic() - Method in class Channel: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class BoundedVoxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class Voxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class VoxelsUntyped: Interface that allows manipulation of voxel intensities via arithmetic operations.
ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
ArithmeticWithConstantBase() - Constructor for class ArithmeticWithConstantBase
ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
ArithmeticWithConstantConditionallyWriteBase() - Constructor for class ArithmeticWithConstantConditionallyWriteBase
ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack: Creates a stack that tiles (or otherwise combines) other providers
ArrangeRaster(boolean, boolean) - Constructor for class ArrangeRaster
ArrangeRaster() - Constructor for class ArrangeRaster
ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
ArrangeStackBean() - Constructor for class ArrangeStackBean
ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
ArrangeStackException(String) - Constructor for exception ArrangeStackException
ArrangeStackException(Exception) - Constructor for exception ArrangeStackException
array() - Method in class UnsignedByteBuffer: The array of the buffer ala ByteBuffer.array().
array() - Method in class UnsignedIntBuffer: The array of the buffer ala IntBuffer.array().
array() - Method in class UnsignedShortBuffer: The array of the buffer ala ShortBuffer.array().
as(boolean) - Static method in enum OutsideKernelPolicy: Multiplexes between OutsideKernelPolicy.AS_ON and OutsideKernelPolicy.AS_OFF.
asArray(boolean) - Static method in class RGBChannelNames: Creates an array with all channel-names in R-G-B order.
asByte() - Method in class BinaryValuesInt: Derives a BinaryValuesByte representation from the current values.
asByte() - Method in class VoxelsUntyped: Casts to use a UnsignedByteBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
asCollection() - Method in class StackSeries
AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
AsCollection() - Constructor for class AsCollection
asCollectionOrderNotPreserved() - Method in class ScaledElements: Returns the scaled-elements as a collection but without preserving the original element order.
asExtent() - Method in class SizeXY: Creates an extent with identical width and height and depth (z-extent) of 1
asExtent(int) - Method in class SizeXY: Creates an extent with identical width and height and a specific depth (z-extent)
asFile() - Method in interface InputFromManager: Expresses the input as a file with a name (the unique identifier).
asFloat() - Method in class VoxelsUntyped: Casts to use a FloatBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asFloat(ImageProcessor) - Static method in class ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<FloatBuffer>
asGraph() - Method in class IntersectingObjects: Constructs a graph where each vertex is an element and an edge exists between any elements that intersect.
asInt() - Method in class BinaryValuesByte: Derives a BinaryValuesInt representation from the current values.
asInt() - Method in class VoxelsUntyped: Casts to use a UnsignedIntBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asList() - Method in class StringList: Exposes the underlying list of values.
asList() - Method in class FeatureList: Exposes the underlying list of features in this data-structure.
asList() - Method in class FeatureNameList: Exposes the underlying list of names.
asList(boolean) - Static method in class RGBChannelNames: Creates a list with all channel-names in R-G-B order.
asList() - Method in class ObjectCollection: Exposes the underlying objects as a list.
asList() - Method in class OverlayCollection
asListChannels() - Method in class Stack: Derives a List of Channels from those in the Stack, preserving order.
asListOrderPreserved(List<T>) - Method in class ScaledElements: Returns a list of scaled-elements corresponding to a list of unscaled-elements.
asMap() - Method in class ScaledElements: The underlying map used to map an unscaled object to its scaled counterpart.
AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
AsMark() - Constructor for class AsMark
asMarks() - Method in class EnergyMemoList
asNamedStacks() - Method in class NamedStacksUniformSize: Exposes the stacks as a NamedStacks.
AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
AsObject() - Constructor for class AsObject
asObjectMask() - Method in class ObjectWithProperties: Exposes the underlying ObjectMask ignoring any properties.
AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask feature
AsObjectMask() - Constructor for class AsObjectMask
asOperationFailedException() - Method in exception GetOperationFailedException: Converts to a OperationFailedException using an identical message.
asPath() - Method in class RootPath: Exposes the path field as a Path.
asPath(boolean) - Method in class DirectoryWithPrefix: A path that combines the directory and fileNamePrefix and delimiter.
asPoint() - Method in class Padding
asPredicateDouble() - Method in class RelationToThreshold: Expresses the relation as a predicate on values, where only values that fulfill the relation to threshold are true.
asPredicateInt() - Method in class RelationToThreshold: Like RelationToThreshold.asPredicateDouble() but expresses the relationship for an integer.
asScaleFactor() - Method in class ScaleFactorInt: Converts to a ScaleFactor that accepts floating-point values.
assertCalc(ResultsVector, Object...) - Static method in class ResultsVectorTestUtilities
assertDoubleResult(String, Feature<T>, T, double) - Static method in class FeatureTestCalculator
assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class FeatureTestCalculator
assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class FeatureTestCalculatorDuo
assertIntResult(String, Feature<T>, T, int) - Static method in class FeatureTestCalculator
assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class FeatureTestCalculator
assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class FeatureTestCalculatorDuo
assertValid() - Method in class MarksWithEnergyBreakdown
assertValid() - Method in class EnergySavedInd
assertValid() - Method in class EnergySavedPairs
asSet(boolean) - Static method in class RGBChannelNames: Creates a set of the channel names.
asSet(Progress, Logger) - Method in interface ProvidesStackInput: Exposes the input as a set of named stacks (inferring the names).
asSet() - Method in class RTree: All elements contained within the tree, as a Set.
asShort() - Method in class VoxelsUntyped: Casts to use a UnsignedShortBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asShort(ImageProcessor) - Static method in class ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
assignAccepted(DualMarks) - Method in class DualMarksAnnotation: Assigns marks with an overall accepted state.
assignBestFromCurrent() - Method in class DualState
assignBoundingBox(BoundingBox) - Method in class BoundedList: Assigns a new containing bounding-box.
assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class BoundedList: Assigns a new containing bounding-box and maps each individual element.
assignColor(Point3i, RGBColor) - Method in class RGBStack: Assigns a RGBColor to the respective channels for a single voxel.
assignCopyNonInputs() - Method in class InputArguments
assignCurrent(Optional<T>) - Method in class DualState
assignDescription(ManifestDirectoryDescription) - Method in class MutableDirectory: Assigns a description, which may not already exist.
assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class IterateVoxelsAll: Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
AssignerMatchClass - Class in org.anchoranalysis.bean.initializable.property: Allows assignment of parameters if they are are of type paramTypeMatch or subclass of it.
AssignerMatchClass(Class<?>) - Constructor for class AssignerMatchClass
AssignFeatureNameUtilities - Class in org.anchoranalysis.feature.name: Utilities for assigning a name to a feature.
assignFilterExtensions(Set<String>) - Method in class InputArguments
assignFilterExtensionsIfMissing(Optional<Set<String>>) - Method in class InputArguments
assignFilterGlob(String) - Method in class InputArguments
assignFrom(Mark) - Method in class VoxelizedMarkMemo: Assigns a new mark to replace the existing mark.
AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Copies the pixels from channelAssignFrom to channel (possibly masking)
AssignFromChannel() - Constructor for class AssignFromChannel
AssignFromDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
AssignFromDictionary() - Constructor for class AssignFromDictionary
AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
AssignFromIntersectingObjects() - Constructor for class AssignFromIntersectingObjects
assignFunction(String) - Method in class ManifestDescription: Assigns a new function.
assignIdentifierSubrange(IndexRangeNegative) - Method in class InputArguments: If defined, this indicates and specifies only a subset of the elements of the identifier to use.
assignInitializationToProperties(Object, Object, Object, Logger) - Method in class AssignerMatchClass
assignInitializationToProperties(Object, Object, Object, Logger) - Method in interface InitializationParameterAssigner: Assigns the parameter to the bean.
assignInputDirectory(Optional<Path>) - Method in class InputArguments: Sets an input-directory.
assignLogger(Logger) - Method in class OutputterChecked: Assigns a logger to the outputter, which is used to output warnings or messages when outputting.
assignMaximumIndex(int) - Method in class IncreasingIntegers
assignMaximumIndex(int) - Method in class IncrementingIntegers
assignMaximumIndex(int) - Method in class SequenceType: If the sequence-type supports a different maximum-index to that derived from the elements SequenceType.update(T), this assigns it.
assignMaximumIndex(int) - Method in class StringsWithoutOrder
assignMaxNumberProcessors(String) - Method in class TaskArguments
Assignment<T> - Interface in org.anchoranalysis.annotation.io.assignment: A one-to-one pairing between items in two respective sets.
AssignmentColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator: Different ColorSchemes that can be used to select colors for paired and unpaired objects.
AssignmentColorPool(int, ColorScheme) - Constructor for class AssignmentColorPool: Creates with a number and colors for the paired objects, and defaults colors for unpaired.
AssignmentColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class AssignmentColorPool
AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator: Outputs a raster showing an Assignment on a background.
AssignmentGenerator(DrawColoredObjects, IntFunction<AssignmentColorPool>, Tuple2<String, String>, boolean) - Constructor for class AssignmentGenerator
AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: How assignments and other decisions are made in the SimulatedAnnealing optimizaton
AssignMode() - Constructor for class AssignMode
assignModelDirectory(Path) - Method in class InputArguments
assignName(String) - Method in class ClusterIdentifier: Assigns a name for the cluster.
assignOff() - Method in class Mask: Interface that allows assignment of an off state to all or subsets of the voxels.
assignOff() - Method in class BinaryVoxels: Creates an assigner that may set the off state in subsequently specified regions of the voxels.
assignOff() - Method in class ObjectMask: Assigns the off value to voxels, expecting global coordinates.
assignOn() - Method in class Mask: Interface that allows assignment of an on state to all or subsets of the voxels.
assignOn() - Method in class BinaryVoxels: Creates an assigner that may set the on state in subsequently specified regions of the voxels.
assignOn() - Method in class ObjectMask: Assigns the on value to voxels, expecting global coordinates.
assignOutputDirectory(Path) - Method in class OutputPrefixerSettings
AssignOverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment: Creates a one-to-one assignment between two sets of ObjectMasks.
AssignOverlappingObjects(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class AssignOverlappingObjects
assignParentDirectory(Optional<MutableDirectory>) - Method in class MutableDirectory
assignPath(Path) - Method in class SubdirectoryBase
assignPaths(List<Path>) - Method in class InputArguments
assignPaused(DualMarks) - Method in class DualMarksAnnotation: Assigns marks with an overall paused state.
AssignPermutationException - Exception in org.anchoranalysis.bean.permute.assign: When the assignment of a permuted value to a property cannot succeed.
AssignPermutationException(String) - Constructor for exception AssignPermutationException: Create with an error message.
assignPrevious(double, int) - Method in class UnchangedBase: Assigns the previous value to be remembered for comparison next time.
assignPrevious(double, int) - Method in class UnchangedScore
assignPrevious(double, int) - Method in class UnchangedSize
AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
AssignPriority() - Constructor for class AssignPriority
assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class AssignPriority: Assigns a priority to a potential merge
AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority: Allows merges if there is an increase in the payload i.e.
AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class AssignPriorityFromImprovement
AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority: Calculates pair-feature on each potential merge, and this value determines priority..
AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, DoubleBiPredicate) - Constructor for class AssignPriorityFromPair
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriority
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromImprovement
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromPair
assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in interface KernelAssigner
assignProposal(Optional<T>, KernelWithIdentifier<S, V>) - Method in class OptimizationStep
assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in class KernelAssignerAddErrorLevel
assignProposal(OptimizationStep<S, T, V>, TransformationContext, KernelWithIdentifier<S, V>) - Method in class KernelAssignerCalculateEnergyFromKernel
assignRejected(DualMarks, T) - Method in class DualMarksAnnotation: Assigns marks with an overall rejected state.
assignRelativeForIdentifier() - Method in class InputArguments
assignResolution(Optional<Resolution>) - Method in class Channel: Assigns a new resolution.
assignResolution(Resolution) - Method in class Stack: Assigns a new resolution.
assignShuffle() - Method in class InputArguments
assignSize(String) - Method in class TaskArguments
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputArguments
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputPrefixerSettings
assignTaskName(Optional<String>) - Method in class TaskArguments
assignTo(Feature<FeatureInput>) - Method in class Feature: Copies fields in this (base) class to target.
assignTo(KernelPosNeg<T, S>) - Method in class KernelPosNeg: Copies fields in this (base) class to target.
assignTo(ConicFitterBase) - Method in class ConicFitterBase: Copies fields in this (base) class to target.
assignType(String) - Method in class ManifestDescription: Assigns a new type.
assignValue(AnchorBean<?>, Object) - Method in interface PermutationAssigner: Assigns value to one or more properties in bean.
assignValue(int) - Method in class Channel: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class BoundedVoxels: Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
assignValue(int) - Method in class Voxels: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class VoxelsFloat
assignValue(int) - Method in class VoxelsUnsignedByte
assignValue(int) - Method in class VoxelsUnsignedInt
assignValue(int) - Method in class VoxelsUnsignedShort
assignValue(int) - Method in class VoxelsUntyped: Interface that allows assignment of a particular value to all or subsets of the voxels.
AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Assigns a constant (scalar) value to the portion of the image covered by a mask
AssignValue() - Constructor for class AssignValue
assignWithPrefix(Feature<? extends FeatureInput>, String, String) - Static method in class AssignFeatureNameUtilities: Assigns a new custom-name to a feature, by combining an existing-name with a prefix.
AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element: Extracts one of the memos from the pair, and processes as a FeatureSingleMemo
AsSingle() - Constructor for class AsSingle
AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
AsSingleMark() - Constructor for class AsSingleMark
associated - Variable in class AddOptionsFromCommandLine: An associated entity which consumers accept.
associatedFile() - Method in class AnnotationWithStrategy: The file associated with the annotation, if such a file exists.
AssociatedIndex - Interface in org.anchoranalysis.core.index: Associated an index with the object.
associateFileWithCluster(File, long, ClusterIdentifier) - Method in class ClusterMembership: Indicates a particular file is a member of a particular cluster.
associateXML(XMLConfiguration) - Method in interface AssociateXMLUponLoad: Associated an XML configuration with an object.
associateXML(XMLConfiguration) - Method in class Experiment
associateXML(XMLConfiguration) - Method in class QuickMultiDatasetStructuredExperiment
AssociateXMLUponLoad - Interface in org.anchoranalysis.bean.xml: For classes that wish to have a XmlConfiguration associated with them.
asStack() - Method in class EnergyStack: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class EnergyStackWithoutParameters: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class RGBStack: Exposes the underlying stack, storing the three RGB channels in respective order.
asTuple() - Method in class Extent: Exposes the extent as a tuple.
asVector3d() - Method in class DirectionVector: Converts to a Vector3d representation.
at(int, int, int, int) - Static method in class BoundingBoxFactory: Short-hand factory method for creating a 2D bounding-box.
at(int, int, int, int, int, int) - Static method in class BoundingBoxFactory: Short-hand factory method for creating a 3D bounding-box.
atanHandlingNan(double) - Static method in class EllipseStandardFormConverter
atBorder(Extent) - Method in class BoundingBox: Does the bounding-box have an edge at the border of an image of size extent?
AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderBase() - Constructor for class AtBorderBase
AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderXY() - Constructor for class AtBorderXY
atBorderXY(Extent) - Method in class BoundingBox: Like BoundingBox.atBorder(Extent) but considers only the X- and Y- dimensions.
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderZ() - Constructor for class AtBorderZ
atBorderZ(Extent) - Method in class BoundingBox: Like BoundingBox.atBorder(Extent) but considers only the Z-dimension.
atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class VoxelsExtracterFactory: Projects a VoxelsExtracter to a corner in a larger global space.
AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates a new object-collection with only a single element (at a particular index) in the existing collection.
AtIndex() - Constructor for class AtIndex
AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
AtLeastZSlices() - Constructor for class AtLeastZSlices
AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation at a different scale, and then fit the results back to the original scale.
AtScale() - Constructor for class AtScale
attachObject(Channel) - Method in class MaxIntensity
attachObject(S) - Method in interface ChannelConverterAttached: Associate the convert with a particular object.
attachObject(Histogram) - Method in class MaxIntensityFromHistogram
attachObject(Histogram) - Method in class QuantileIntensityFromHistogram
attachObject(Histogram) - Method in class UpperLowerQuantileIntensityFromHistogram
AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider: Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
AutoLocalThreshold() - Constructor for class AutoLocalThreshold
Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map: Names of the channels from the metadata if it exists, or after RGB, or by index.
Autoname() - Constructor for class Autoname
Axis - Enum in org.anchoranalysis.spatial.axis: Identifies axis in a Cartesian coordinate system.
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
AxisAlignedUnitVector() - Constructor for class AxisAlignedUnitVector
AxisConversionException - Exception in org.anchoranalysis.spatial.axis: When converting another type to a corresponding Axis fails.
AxisConversionException(String) - Constructor for exception AxisConversionException: Create with a messsage, without an underlying cause.
AxisConverter - Class in org.anchoranalysis.spatial.axis: Converts to/from Axis to a String and int representations, checking for invalid input.
AxisLimits - Class in org.anchoranalysis.plot
AxisLimits() - Constructor for class AxisLimits
AxisLimits(double, double) - Constructor for class AxisLimits
AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature
AxisRatioEllipsoid() - Constructor for class AxisRatioEllipsoid

B

background(DisplayStack) - Method in class MarksFlattenedGenerator
background(DisplayStack) - Method in class MarksGenerator
background(DisplayStack) - Method in class MarksGeneratorBase
BackgroundCreator - Class in org.anchoranalysis.mpp.io.output
BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
BackgroundSubtractor() - Constructor for class BackgroundSubtractor
BarPlot<T> - Class in org.anchoranalysis.plot.index: A bar plot, stacked or non-stacked.
BarPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, Double>, GetForSeries<T, Paint>, boolean) - Constructor for class BarPlot
BBoxRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
BBoxRatio() - Constructor for class BBoxRatio
BeanCreator - Class in org.anchoranalysis.bean.xml.creator: Creates a single AnchorBean from XML.
BeanDuplicateException - Exception in org.anchoranalysis.bean.exception: An exception occurs when the duplication of a bean fails.
BeanDuplicateException(String) - Constructor for exception BeanDuplicateException: Creates with a message only.
BeanDuplicateException(Throwable) - Constructor for exception BeanDuplicateException: Creates with a cause only.
BeanDuplicateException(String, Throwable) - Constructor for exception BeanDuplicateException: Creates with a message and cause.
BeanField - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a field in an Anchor Bean class is to be treated as a bean-field.
BeanInitialization - Interface in org.anchoranalysis.bean.initializable.parameters: Parent class for all state used to initialise beans in InitializableBean.
BeanInitializer - Class in org.anchoranalysis.bean.initializable.property: Tries to initialize a bean and it's children with particular parameters, if possible.
BeanInitializer(Class<?>) - Constructor for class BeanInitializer: Simpler case where only the current-parameters can be initialized, but for no further property-types.
BeanInitializer(Class<?>, List<ExtractDerivedParameter<P, ?>>) - Constructor for class BeanInitializer: More complex-case where both current-parameters and other extracted property-types can be initialized.
BeanInstanceMap - Class in org.anchoranalysis.bean: Maps a AnchorBean family-type to a bean that belongs to the family.
BeanInstanceMap() - Constructor for class BeanInstanceMap
BeanListCreator - Class in org.anchoranalysis.bean.xml.creator: Like BeanCreator but creates a list of beans.
BeanMisconfiguredException - Exception in org.anchoranalysis.bean.exception: If a Bean is misconfigured.
BeanMisconfiguredException(String) - Constructor for exception BeanMisconfiguredException: Creates with a message only.
BeanMisconfiguredException(String, Throwable) - Constructor for exception BeanMisconfiguredException: Creates with a message and a cause.
BeanMisconfiguredXMLException - Exception in org.anchoranalysis.bean.xml.exception: A bean's XML is thrown when a bean has misconfigured XML.
BeanMisconfiguredXMLException(String, Throwable) - Constructor for exception BeanMisconfiguredXMLException: Constructor
BeanMisconfiguredXMLException(Throwable) - Constructor for exception BeanMisconfiguredXMLException: Constructor
BeanPathCalculator - Class in org.anchoranalysis.bean.xml.factory: Calculates file-system paths involving an AnchorBean.
BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider: A provider base-class that as well as providing type S, also provides a Stack.
BeanProviderAsStackBase() - Constructor for class BeanProviderAsStackBase
BeanStrangeException - Exception in org.anchoranalysis.bean.exception: When something quite strange happens that we don't usually want to catch.
BeanStrangeException(String) - Constructor for exception BeanStrangeException: Creates with a message only.
BeanStrangeException(String, Throwable) - Constructor for exception BeanStrangeException: Creates with a message and cause.
BeanTestChecker - Class in org.anchoranalysis.test.experiment: Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping the usual checks during the BeanXML loading process).
BeanXMLException - Exception in org.anchoranalysis.bean.xml.exception: An exception that occurs when one cannot process BeanXML for some reason.
BeanXMLException(String) - Constructor for exception BeanXMLException: Creates with a message only.
BeanXMLException(Throwable) - Constructor for exception BeanXMLException: Creates with a cause only.
BeanXMLException(String, Throwable) - Constructor for exception BeanXMLException: Creates with a message and cause.
BeanXMLLoader - Class in org.anchoranalysis.bean.xml: Creates beans based on XML specifying their properties (including nested children).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class Task: Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class TaskWithoutSharedState
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationWithStrategy<S>>, ParametersExperiment) - Method in class AggregateAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>>, ParametersExperiment) - Method in class CompareAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ExportFeatures
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ConvertImageFormat
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class GroupedStackBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class ImageAssignLabel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class ScaleImage
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class SegmentInstanceWithModel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class ExtractSlice
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class MovieFromSlices
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileInput>, ParametersExperiment) - Method in class CombineCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileWithDirectoryInput>, ParametersExperiment) - Method in class CopyFiles
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class SummarizeBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class ConvertNamedChannels
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ManifestCouplingDefinition>, ParametersExperiment) - Method in class ExportReportFeaturesFromManifest
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportReportFeaturesFromMulti
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class ExportObjectsAsCroppedImages
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FromCSVInput>, ParametersExperiment) - Method in class ExportObjectsFromCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<MultiInput>, ParametersExperiment) - Method in class SegmentMarksFromImage
beforeCalc(FeatureInitialization) - Method in class Feature: Dummy method, that children can optionally override.
beforeCalc(FeatureInitialization) - Method in class ConvertToPhysicalDistance
beforeCalc(FeatureInitialization) - Method in class FeatureIntersectingObjects
beforeCalc(FeatureInitialization) - Method in class PairedWithMask
beforeCalc(FeatureInitialization) - Method in class FeatureSingleObjectFromShared
beforeCalc(FeatureInitialization) - Method in class ParamFromCollection
beforeCalc(FeatureInitialization) - Method in class FeatureMarkDirection
beforeCalc(FeatureInitialization) - Method in class FromDictionary
beforeCalcSetup(Histogram, int) - Method in class CalculateLevel
beforeCalcSetup(Histogram, int) - Method in class CalculateLevelBase
beforeCalcSetup(Histogram, int) - Method in class DifferenceCalculateLevelStandardDeviation
beforeCalcWithInitialization(ImageInitialization) - Method in class FeatureSingleObjectFromShared
beforeCalcWithInitialization(ImageInitialization) - Method in class MaskAsSingleObject
beforeCalcWithInitialization(ImageInitialization) - Method in class ObjectAggregationBase
BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class Anonymize
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class ClusterByTimestamp
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class CopyFilesNaming: To be called once before any calls to CopyFilesNaming.destinationPath(File, DirectoryWithPrefix, int, CopyContext).
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class CopyFilesNamingOne
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class CopyFilesNamingWithoutSharedState
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class PreserveName
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitScheduler
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerAnd
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerConvexAboutRoot
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerMaxDistanceAlongContour
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class VisitSchedulerUniformSample
binaryChannel(boolean) - Static method in class StackWriteAttributesFactory
BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
BinaryClassifierImageLabeller() - Constructor for class BinaryClassifierImageLabeller
BinaryKernel - Class in org.anchoranalysis.image.voxel.kernel: Base class for kernels that return a boolean for every voxel.
BinaryKernel(int) - Constructor for class BinaryKernel: Creates with a specific kernel-size.
BinaryKernelMorphological - Class in org.anchoranalysis.image.voxel.kernel.morphological: A parent class for any BinaryKernel that implements a morphological operation.
BinaryKernelMorphological(boolean, boolean, boolean) - Constructor for class BinaryKernelMorphological: Creates with a flag for big-neighborhood, and boolean outcomes for certain cases.
BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects anything that is not off voxels from a binary mask.
BinaryNotOffVoxels() - Constructor for class BinaryNotOffVoxels
BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects anything that is not on voxels from a binary mask.
BinaryNotOnVoxels() - Constructor for class BinaryNotOnVoxels
BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the off voxels from a binary mask.
BinaryOffVoxels() - Constructor for class BinaryOffVoxels
BinaryOnOffSetter - Interface in org.anchoranalysis.image.voxel.binary: Getters and setters for reading and assigning binary state to voxels.
BinaryOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the on pixels from a binary mask.
BinaryOnVoxels() - Constructor for class BinaryOnVoxels
binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperation) - Static method in class IterateVoxelsAll: Iterate over each voxel in a bounding-box - applying a binary operation with values from two input Voxels<UnsignedByteBuffer> for each slice and writing it into an output Voxels<UnsignedByteBuffer>.
BinaryOutcomeImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
BinaryOutcomeImageLabeller() - Constructor for class BinaryOutcomeImageLabeller
binaryResizing(int) - Method in class InterpolatorFactory: An Interpolator that is suitable for resizing a binary raster-image, restricted to two possible intensity values only.
BinarySegmentation - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentation() - Constructor for class BinarySegmentation
BinarySegmentationOne - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationOne() - Constructor for class BinarySegmentationOne
BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment: Parameters that are optionally associated with a BinarySegmentation
BinarySegmentationParameters() - Constructor for class BinarySegmentationParameters
BinarySegmentationParameters(Optional<Resolution>) - Constructor for class BinarySegmentationParameters
BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class BinarySegmentationParameters: Constructor
BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class BinarySegmentationParameters
BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationReference() - Constructor for class BinarySegmentationReference
binarySegmentations() - Method in class ImageInitialization
BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationThreshold() - Constructor for class BinarySegmentationThreshold
BinarySegmentByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs a binary-segmentation using the upstream objects as masks.
BinarySegmentByObject() - Constructor for class BinarySegmentByObject
binaryValues() - Method in class BinaryVoxels: Which two intensity values represent off and on states.
binaryValues() - Method in class ObjectMask: What values constitute an on and off state in voxels - as ints.
binaryValuesByte() - Method in class Mask: The two states which are permitted to be assigned to the voxels, stored as bytes.
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing byte binary states in an UnsignedByteBuffer.
BinaryValuesByte(int, int) - Constructor for class BinaryValuesByte: Create with int values for off and on states.
BinaryValuesByte(byte, byte) - Constructor for class BinaryValuesByte
binaryValuesByte() - Method in class ObjectMask: What values constitute an on and off state in voxels - as bytes.
binaryValuesInt() - Method in class Mask: The two states which are permitted to be assigned to the voxels, stored as unsigned ints.
BinaryValuesInt - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing int binary states in an unsigned-byte buffer.
BinaryValuesInt(int, int) - Constructor for class BinaryValuesInt
binaryVoxels() - Method in class Mask: The underlying voxels in the mask, exposed as BinaryVoxels.
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary: Like Voxels but should only contain two distinct intensity-values representing on and off.
BinaryVoxels(Voxels<T>, BinaryValuesInt) - Constructor for class BinaryVoxels
binaryVoxels() - Method in class ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via a BinaryVoxels.
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation
BinaryVoxelsBase() - Constructor for class BinaryVoxelsBase
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary: Creates BinaryVoxels parameterized by size and initial state.
binaryVoxelsFor(Voxels<T>, BinaryValuesInt) - Method in class BinaryVoxels: Creates a BinaryVoxels corresponding to a particular voxels and BinaryValuesInt.
bind(FeatureList<T>, FeatureInitialization, SharedFeatures, Logger) - Method in class BoundReplaceStrategy
BindFailedException - Exception in org.anchoranalysis.io.output.outputter
BindFailedException(String) - Constructor for exception BindFailedException
BindFailedException(Throwable) - Constructor for exception BindFailedException
BioformatsReader - Class in org.anchoranalysis.io.bioformats.bean: Reads a stack using the Bioformats library.
BioformatsReader(ReadOptions) - Constructor for class BioformatsReader: Create with particular options.
BioformatsReader() - Constructor for class BioformatsReader
BioformatsWriter - Class in org.anchoranalysis.io.bioformats.bean.writer: Base class for writing a stack to the filesystem using the Bioformats library.
BioformatsWriter(boolean) - Constructor for class BioformatsWriter
bitDepth(Logger) - Method in class NamedChannelsInput: Bit-depth of image.
bitDepth(Logger) - Method in interface OpenedImageFile: The bit-depth of the image voxels e.g.
bitDepth() - Method in class VoxelDataType: The number of bits required to represent a voxel.
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
BitDepth() - Constructor for class BitDepth
bitDepth(Logger) - Method in class OpenedMultiFile
BitDepthPerChannel - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The bit-depth of the image per channel.
BitDepthPerChannel() - Constructor for class BitDepthPerChannel
BlackBackgroud - Class in org.anchoranalysis.plot.bean.colorscheme: A black background and white axes.
BlackBackgroud() - Constructor for class BlackBackgroud
blockUntilLoaded() - Static method in class CVInit: Blocks a thread until the initialization has completed.
BLUE - Static variable in class RGBChannelNames: Name for the blue channel.
blue() - Method in class RGBStack: The blue channel.
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class BlurGaussian3D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class BlurGaussianEachSlice2D
blur(VoxelsUntyped, Dimensions, MessageLogger) - Method in class BlurStrategy
Blur - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Blur() - Constructor for class Blur
BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian Blur in 3D
BlurGaussian3D() - Constructor for class BlurGaussian3D
BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian-blur in 2D on each slice independently
BlurGaussianEachSlice2D() - Constructor for class BlurGaussianEachSlice2D
BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur: A method for applying blurring to an image
BlurStrategy() - Constructor for class BlurStrategy
BMP - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a BMP file.
BMP() - Constructor for class BMP
bothNameAndParameters() - Static method in class NamedFeatureStoreFactory: The custom-names of the features are derived from both their name and their parameters.
Bound - Class in org.anchoranalysis.mpp.bean.bound
Bound() - Constructor for class Bound
boundaryMax(FeatureCalculationInput<T>) - Method in class CompareWithRangeFeature
boundaryMax(FeatureCalculationInput<T>) - Method in class RangeCompareBase: Boundary to define the maximum accepted value in the range
boundaryMax(FeatureCalculationInput<T>) - Method in class RangeCompareFromScalars
boundaryMin(FeatureCalculationInput<T>) - Method in class CompareWithRangeFeature
boundaryMin(FeatureCalculationInput<T>) - Method in class RangeCompareBase: Boundary to define the minimum accepted value in the range
boundaryMin(FeatureCalculationInput<T>) - Method in class RangeCompareFromScalars
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound
BoundDegrees() - Constructor for class BoundDegrees
BoundDegrees(BoundDegrees) - Constructor for class BoundDegrees
BoundedList<T> - Class in org.anchoranalysis.spatial.box: One or more elements, each with an individual bounding-box, and collectively with a bounding-box that fully contains them all.
BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel: Voxels that exist within a particular bounding-box in an image.
BoundedVoxels(Voxels<T>) - Constructor for class BoundedVoxels: Creates voxels bounded to match the entire voxel-data at the origin.
BoundedVoxels(BoundedVoxels<T>) - Constructor for class BoundedVoxels: Copy constructor.
BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class BoundedVoxels: Creates voxels with a corresponding bounding box.
boundedVoxels() - Method in class ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via BoundedVoxels.
boundingBox() - Method in class ObjectWithProperties: The bounding-box which gives a location for the object-mask on an image.
boundingBox() - Method in class BoundedVoxels: A bounding-box that associates voxels to a particular part of an image.
boundingBox() - Method in class ObjectMask: The bounding-box which gives a location for the object-mask on an image.
boundingBox() - Method in interface VoxelizedMark: A bounding-box enclosing the voxelized representation of the mark
boundingBox() - Method in class BoundedList: A bounding-box that must contain all elements in the collection
BoundingBox - Class in org.anchoranalysis.spatial.box: A bounding-box in two or three dimensions.
BoundingBox(Extent) - Constructor for class BoundingBox: Constructs a bounding-box to cover the entirety of a certain extent.
BoundingBox(Point3d, Point3d) - Constructor for class BoundingBox: Creates from two double points (a minimum corner and a maximum corner).
BoundingBox(ReadableTuple3i, ReadableTuple3i) - Constructor for class BoundingBox: Creates from two int points (a minimum corner and a maximum corner).
BoundingBox(ReadableTuple3i, Extent) - Constructor for class BoundingBox: Creates a bounding-box from a corner and an extent.
BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxAlongAxisBase() - Constructor for class BoundingBoxAlongAxisBase
BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic: Functions to calculate a bounding-box for a point surrounded by some form of radii
BoundingBoxContains - Class in org.anchoranalysis.spatial.box: Does a bounding box contain other objects?
BoundingBoxContains(BoundingBox) - Constructor for class BoundingBoxContains: Create with the BoundingBox that is queried.
BoundingBoxDistance - Class in org.anchoranalysis.spatial.box: Calculates distance between two bounding boxes.
BoundingBoxesOnPlane - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Describes a set of bounding boxes on top of a plane
BoundingBoxesOnPlane(Extent, BoundingBox) - Constructor for class BoundingBoxesOnPlane
BoundingBoxesOnPlane(Extent) - Constructor for class BoundingBoxesOnPlane
BoundingBoxExtent - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
BoundingBoxExtent() - Constructor for class BoundingBoxExtent
BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxExtentAlongAxis() - Constructor for class BoundingBoxExtentAlongAxis
BoundingBoxFactory - Class in org.anchoranalysis.spatial.box: Utility methods to create a BoundingBox.
boundingBoxFlattened() - Method in interface VoxelizedMark: The bounding-box flattened in z dimension
boundingBoxFor(T) - Method in interface AccessObjectMask: A bounding-box for a given element.
boundingBoxForRegion(VoxelizedMark) - Method in class IndexedRegionBase
BoundingBoxFromPoints - Class in org.anchoranalysis.image.core.points: Creates a bounding-box from one or more points.
BoundingBoxIntersection - Class in org.anchoranalysis.mpp.feature.addcriteria
BoundingBoxIntersection() - Constructor for class BoundingBoxIntersection
BoundingBoxIntersection - Class in org.anchoranalysis.spatial.box: Methods for checking intersection between a particular bounding-box and others.
BoundingBoxIntersection(BoundingBox) - Constructor for class BoundingBoxIntersection
BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxMaximumAlongAxis() - Constructor for class BoundingBoxMaximumAlongAxis
BoundingBoxMerger - Class in org.anchoranalysis.spatial.box: Merges one or more BoundingBox together, to create a single BoundingBox that spans them all.
BoundingBoxMinimumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxMinimumAlongAxis() - Constructor for class BoundingBoxMinimumAlongAxis
BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxNumberVoxels() - Constructor for class BoundingBoxNumberVoxels
BoundingBoxOutline - Class in org.anchoranalysis.image.io.bean.object.draw: Draws the outline of the bounding-box for each object.
BoundingBoxOutline() - Constructor for class BoundingBoxOutline
BoundingBoxOutline(int) - Constructor for class BoundingBoxOutline
BoundingBoxRTree<T> - Class in org.anchoranalysis.spatial.rtree: An R-Tree that contains items, each with an associated bounding-box in three dimensions.
BoundingBoxRTree() - Constructor for class BoundingBoxRTree: Creates an empty R-Tree.
BoundingBoxRTree(int) - Constructor for class BoundingBoxRTree: Creates an empty R-Tree with a specified number of children.
boundingBoxThatSpansInput(T) - Method in class CombineObjectsForFeatures: Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects)
boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class EachObjectIndependently
boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class PairNeighbors
BoundingBoxUnion - Class in org.anchoranalysis.spatial.box: Performs union of a bounding-box with other entities
BoundingBoxUnion(BoundingBox) - Constructor for class BoundingBoxUnion
BoundingBoxZDistance - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Measures the amount of distance in Z for the bounding box.
BoundingBoxZDistance() - Constructor for class BoundingBoxZDistance
BoundingBoxZOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Measures the amount of bounding box overlap in the Z dimension
BoundingBoxZOverlapRatio() - Constructor for class BoundingBoxZOverlapRatio
BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound
BoundMinMax() - Constructor for class BoundMinMax
BoundMinMax(double, double) - Constructor for class BoundMinMax
BoundMinMax(BoundMinMax) - Constructor for class BoundMinMax
BoundOutputter<T> - Class in org.anchoranalysis.io.generator.sequence: An outputter bound together with OutputPattern and a generator.
BoundOutputter(OutputterChecked, OutputPattern, Generator<T>) - Constructor for class BoundOutputter
BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound
BoundPhysicalExtent(double, double) - Constructor for class BoundPhysicalExtent
BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class BoundPhysicalExtent
BoundPhysicalExtent() - Constructor for class BoundPhysicalExtent
BoundReplaceStrategy<T extends FeatureInput,S extends ReplaceStrategy<T>> - Class in org.anchoranalysis.feature.session.replace: Attaches a replacement-strategy to a session lazily (i.e.
BoundReplaceStrategy(Function<CacheCreator, S>) - Constructor for class BoundReplaceStrategy
BoundRotation - Class in org.anchoranalysis.mpp.bean.bound.rotation
BoundRotation() - Constructor for class BoundRotation
BoundRotation2D - Class in org.anchoranalysis.mpp.bean.bound.rotation: Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
BoundRotation2D() - Constructor for class BoundRotation2D
BoundRotation3D - Class in org.anchoranalysis.mpp.bean.bound.rotation: Creates a randomly-generated orientation in 3D based upon Euler Angles
BoundRotation3D() - Constructor for class BoundRotation3D
BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound
BoundUnitless() - Constructor for class BoundUnitless
BoundUnitless(double, double) - Constructor for class BoundUnitless
BoundUnitless(BoundUnitless) - Constructor for class BoundUnitless
box(Dimensions, int) - Method in class Ellipse
box(Dimensions, int) - Method in class Ellipsoid
box(Dimensions, int) - Method in class MarkWithPositionAndSingleRadius
box(Dimensions, int) - Method in class Mark
box(Dimensions, int) - Method in class LineSegment
box(Dimensions, int) - Method in class PointListBase
box() - Method in class PointListBase
box(Dimensions, int) - Method in class RotatableBoundingBox
box(DrawOverlay, Dimensions) - Method in class OverlayMark: How we create our scaled masks
box(DrawOverlay, Dimensions) - Method in class OverlayObjectMask
box(DrawOverlay, Dimensions) - Method in class Overlay: A bounding-box around the overlay
Box - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Creates a Mask where all pixels are on within a box region.
Box() - Constructor for class Box
box(FeatureInputPairMemo, Function<FeatureInputPairMemo, VoxelizedMarkMemo>) - Method in class FeaturePairMemoSingleRegion
box(BoundingBox) - Method in class BoundingBoxContains: Is this other bounding-box fully contained within this bounding box?
boxAllRegions(Dimensions) - Method in class Ellipse
boxAllRegions(Dimensions) - Method in class Ellipsoid
boxAllRegions(Dimensions) - Method in class MarkWithPositionAndSingleRadius
boxAllRegions(Dimensions) - Method in class Mark
boxAllRegions(Dimensions) - Method in class LineSegment
boxAllRegions(Dimensions) - Method in class PointList
boxAllRegions(Dimensions) - Method in class Polygon
boxAllRegions(Dimensions) - Method in class PolygonCurve
boxAllRegions(Dimensions) - Method in class RotatableBoundingBox
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter: Copies a bounding-box area to another Voxels.
boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class BoundingBoxCalculator: Calculates a bounding box for a point with a scalar radius in all dimensions.
boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class BoundingBoxCalculator: Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
boxIterator() - Method in class BoundingBoxesOnPlane
boxList(Dimensions, int) - Method in class MarkCollection
boxList(DrawOverlay, Dimensions) - Method in class ColoredOverlayCollection
boxList(DrawOverlay, Dimensions) - Method in class OverlayCollection
BoxPlot<T> - Class in org.anchoranalysis.plot.index
BoxPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, BoxAndWhiskerItem>, GetForSeries<T, Paint>) - Constructor for class BoxPlot
BranchChannels - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on the number/type of channels.
BranchChannels() - Constructor for class BranchChannels
BranchExtension - Class in org.anchoranalysis.plugin.io.bean.stack.reader: If the extension(s) of a path matches a particular value, then use a particular reader, otherwise a fallback.
BranchExtension() - Constructor for class BranchExtension
BranchIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Uses one input-manager normally, but a different one if in debug mode.
BranchIfDebug() - Constructor for class BranchIfDebug
BranchStack - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
BranchStack() - Constructor for class BranchStack
BranchSuggestedFormat - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Selects particular writers based on if particular suggested image formats are present.
BranchSuggestedFormat() - Constructor for class BranchSuggestedFormat
Bridge - Class in org.anchoranalysis.plugin.image.bean.object.match: Matches to another object, and then uses that object to bridge to another
Bridge() - Constructor for class Bridge
buffer() - Method in class VoxelBuffer: The associated buffer for storing the voxels.
buffer() - Method in class VoxelBufferUnsigned
BufferedImageFromStack - Class in org.anchoranalysis.image.core.bufferedimage: Converts a Stack or similar data-objects into an AWT BufferedImage.
BufferedImageFromVoxels - Class in org.anchoranalysis.image.voxel.convert.bufferedimage: Converts a Voxels instance into an AWT BufferedImage.
bufferRelative(int) - Method in class SlidingBuffer: Returns the corresponding buffer at a relative z-slice index to the current focused z-slice.
BufferRetriever - Interface in org.anchoranalysis.image.voxel.kernel: Retrieves a buffer corresponding to a relative index in the z-dimension.
buildPath(String) - Method in interface FileFormat: Builds a path which has an existing path but missing an extension.
buildPath(Path) - Method in interface FileFormat: Builds a path which has an existing path but missing an extension.
buildPath(Path, String) - Method in interface FileFormat: Builds a path with a directory and filename component.
buildPath(String, String) - Method in interface FileFormat: Builds a path with a directory and filename component.
buildPath(String, String, String) - Method in interface FileFormat: Builds a path with a directory, subdirectory, and filename component.
bySymbol() - Method in interface FeatureCalculationInput: Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.
bySymbol() - Method in class SessionInputSequential
ByteRepresentationForChannel - Interface in org.anchoranalysis.io.bioformats.bean.writer: Creates or retrieves a byte representation of the voxels for a particular slice.
bytesForSlice(int) - Method in interface ByteRepresentationForChannel: The byte-representation of the voxels for a particular slice.
bytesPerVoxel() - Method in class ConvertTo: The number bytes to describe each source-voxel.
bytesPerVoxel() - Method in class UnsignedByteFromFloat
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedByte
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedByteNoInterleavingScale
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedInt
bytesPerVoxel() - Method in class UnsignedByteFromUnsignedShort
bytesPerVoxel() - Method in class FloatFromUnsignedByte
bytesPerVoxel() - Method in class FloatFromUnsignedInt
bytesPerVoxel() - Method in class UnsignedIntFromUnsignedInt
bytesPerVoxel() - Method in class ToUnsignedShort
Bytewise - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: Makes a simple bytewise copy of a file, where no byte is changed.
Bytewise() - Constructor for class Bytewise

C

cache(Supplier<T>) - Static method in class CachedSupplier: Creates a cached-version of a Supplier.
cache(StoreSupplier<T>) - Static method in interface StoreSupplier: Memoizes (caches) the supplied object, and returning it with an identical interface.
cache(CheckedProgressingSupplier<T, E>) - Static method in class CachedProgressingSupplier: Creates a cached-version of a CheckedProgressingSupplier
cache(FeatureCalculatorSingle<T>) - Static method in class FeatureCalculatorCache
cache(FeatureCalculatorSingle<T>, int) - Static method in class FeatureCalculatorCache
cache(FeatureCalculatorMulti<T>) - Static method in class FeatureCalculatorCache
cache(FeatureCalculatorMulti<T>, int) - Static method in class FeatureCalculatorCache
cache(NamedStacksSupplier) - Static method in interface NamedStacksSupplier: Caches a NamedStacksSupplier so that its value will be remembered after first execution.
cache(SerializedObjectSupplier<T>) - Static method in interface SerializedObjectSupplier
CACHE_NAME_FIRST - Static variable in class FeatureDeriveFromPair
CACHE_NAME_MERGED - Static variable in class FeatureDeriveFromPair
CACHE_NAME_SECOND - Static variable in class FeatureDeriveFromPair
CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace: Reuse (without needing to invalidate) an existing session-input as stored in a least-recently used cache, otherwise create a new one.
CacheAndReuseStrategy(CacheCreator) - Constructor for class CacheAndReuseStrategy
cacheChecked(CheckedSupplier<T, E>) - Static method in class CachedSupplier: Creates a cached-version of a CheckedSupplier.
CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache: Creates a FeatureCalculationCache that accepts a particular input type.
CachedProgressingSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.progress: Memoizes (caches) a call to CheckedProgressingSupplier.
CachedSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.cache: Memoizes (caches) a CheckedSupplier.
CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache: Base class for functions that memoize (cache) a call to an interface.
CachedSupplierBase() - Constructor for class CachedSupplierBase
cacheName() - Method in class DerivedObject
cacheName() - Method in class Erode
cacheName() - Method in class Shell
cacheResettable(StoreSupplier<T>) - Static method in interface StoreSupplier: Memoizes (caches) the supplied object, and returning it with a CachedSupplier interface
cachesToAvoidInvalidating() - Method in class CheckCacheForSpecificChildren
cachesToAvoidInvalidating() - Method in interface ChildCacheFinder: If set, these particular-caches are exceptionall NOT invalidated during the typical invalidation operation on their parent.
cachesToAvoidInvalidating() - Method in class DefaultChildCacheFinder
CacheSupplier<T extends FeatureInput,E extends Exception> - Interface in org.anchoranalysis.feature.session.cache.finder
CacheTransferSource<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.finder: An existing cache that can be used as a source for child-caches elsewhere.
CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class CacheTransferSource
CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.cache.finder
CacheTransferSourceCollection() - Constructor for class CacheTransferSourceCollection
calc(FeatureInputMarkCollection) - Method in class FeatureMarkCollection
calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParameters) - Method in class EnergySavedAll
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class MaskAsSingleObject
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class ObjectAggregationBase
calc(FeatureCalculationInput<T>, CalculationPart<U, T>, Function<ResolvedPart<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class CalculateInputFromDelegateOption: Calculates a feature using a cached-calculation as delegate.
calc(FeatureInputMarkCollection) - Method in class NumberMarks
calc(FeatureInputSingleObject, Ellipsoid) - Method in class AxisRatioEllipsoid
calc(FeatureInputSingleObject, Ellipsoid) - Method in class EllipsoidBase
calc(FeatureInputSingleObject, Ellipsoid) - Method in class Ellipsoidicity
calculate(FeatureCalculationInput<T>) - Method in class Feature: Calculates a value for some input.
calculate(FeatureCalculationInput<T>) - Method in class Constant
calculate(FeatureCalculationInput<T>) - Method in class Reference
calculate(FeatureCalculationInput<T>) - Method in class Sum
calculate(FeatureInputResults) - Method in class Count
calculate(FeatureCalculationInput<FeatureInputResults>) - Method in class FeatureResults
calculate(FeatureInputResults) - Method in class FeatureResults: Calculates the feature-result given a FeatureInputResults.
calculate(FeatureInputResults) - Method in class FeatureResultsStatistic
calculate(T) - Method in interface FeatureCalculatorMulti: Calculate the results of the features with a particular input.
calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti: Calculates the results of a subset of the features with a particular input.
calculate(T, ErrorReporter, boolean) - Method in interface FeatureCalculatorMulti: Calculates the results for an input, either calling FeatureCalculatorMulti.calculate(T) or FeatureCalculatorMulti.calculateSuppressErrors(T, org.anchoranalysis.core.log.error.ErrorReporter) depending on a flag.
calculate(T) - Method in class FeatureCalculatorMultiChangeInput
calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
calculate(T) - Method in interface FeatureCalculatorSingle: Calculate the results of the feature with a particular input.
calculate(T) - Method in class FeatureCalculatorSingleChangeInput
calculate(T) - Method in class FeatureCalculatorSingleFromMulti
calculate(Feature<S>, S, ChildCacheName) - Method in interface CalculateForChild: Calculates a feature in a child-cache.
calculate(Feature<S>, CalculationPart<S, T>, ChildCacheName) - Method in interface CalculateForChild: Calculates a feature in a child-cache using a new input created from a CalculationPart.
calculate(ChildCacheName, S, Function<CalculationPartResolver<S>, ResolvedPart<U, S>>) - Method in interface CalculateForChild: Calculates a CalculationPart in a child-cache.
calculate(Feature<T>) - Method in interface FeatureCalculationInput: Calculates the result of a feature using this input.
calculate(FeatureList<T>) - Method in interface FeatureCalculationInput: Calculates the results of several features using this input.
calculate(CalculationPart<S, T>) - Method in interface FeatureCalculationInput: Calculates a feature-calculation after resolving it against the main cache.
calculate(ResolvedPart<S, T>) - Method in interface FeatureCalculationInput: Calculates a resolved Feature-calculation.
calculate(Feature<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator: Calculate the result of feature with a particular input.
calculate(FeatureList<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator: Calculates results for a list of features with a particular input, throwing an exception if a calculation fails.
calculate(T) - Method in class SequentialSession
calculate(T, FeatureList<T>) - Method in class SequentialSession
calculate(Feature<T>) - Method in class SessionInputSequential
calculate(FeatureList<T>) - Method in class SessionInputSequential
calculate(CalculationPart<S, T>) - Method in class SessionInputSequential
calculate(ResolvedPart<S, T>) - Method in class SessionInputSequential
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ScaleCalculator: Calculates a scaling-factor for a source image/entity of particular dimensions.
calculate(FeatureCalculationInput<FeatureInputImageMetadata>) - Method in class FeatureImageMetadata
calculate(ImageMetadata) - Method in class FeatureImageMetadata: Calculates the feature-value for a given ImageMetadata.
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
calculate(FeatureCalculationInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
calculate(FeatureInputObjectCollection) - Method in class FeatureObjectCollection: Calculates the feature-value for a given FeatureInputObjectCollection.
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class First
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Merged
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Minimum
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Second
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberVoxels
calculate(FeatureCalculationInput<T>) - Method in class WithResolutionBase
calculate(int[]) - Method in class VoxelScore
calculate(FeatureInputPairObjects) - Method in class PairsTableCalculator
calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class PairsTableCalculator
calculate(FeatureInputSingleObject) - Method in class SingleTableCalculator
calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class SingleTableCalculator
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class AsSingle
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
calculate(FeatureCalculationInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMark
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ConstantScaleFactor
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class FitTo
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class Invert
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class MinimumXYResolution
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToDimensions
calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToSuggested
calculate(FeatureCalculationInput<T>) - Method in class FromDimensionsBase
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
calculate(ImageMetadata) - Method in class BitDepthPerChannel
calculate(ImageMetadata) - Method in class NumberChannels
calculate(ImageMetadata) - Method in class NumberFrames
calculate(FeatureInputObjectCollection) - Method in class NumberObjects
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Intersection
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class OverlapRelative
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class AtBorderBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class DerivedObject
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class PairedWithMask
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SurfaceNumberVoxelsBase
calculate(int[]) - Method in class Difference
calculate(int[]) - Method in class Identity
calculate(int[]) - Method in class IdentityImposeValueRelationToHistogram
calculate(int[]) - Method in class OutsideRange
calculate(int[]) - Method in class RejectIfIntensityLessThan
calculate(int[]) - Method in class SingleChannel
calculate(FeatureCalculationInput<T>) - Method in class FeatureSingleObjectFromShared
calculate(FeatureCalculationInput<T>) - Method in class ParamFromCollection
calculate(FeatureCalculationInput<T>) - Method in class DataTypeMaxIntensity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class Intensity
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class NumberChannels
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class AsObjectMask
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class QuantileAcrossConnectedComponents
calculate(ObjectMask) - Method in interface PayloadCalculator
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMarkDirection
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class EccentricityAxisAligned
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MaxRatioRadii
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class OrderedRadius
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class RadiiRatio
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class BoundingBoxExtent
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MarkEllipseCircumEstimate
calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class Volume
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsCollection
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsSingleMark
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class CoefficientOfVarianceFromAll
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class MeanFromAll
calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class NumberMarks
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsMark
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsObject
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class BBoxRatio
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Intensity
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MaxSliceArea
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MeanIntensityDifference
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Size
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class SurfaceSizeMaskNonZero
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZDistance
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZOverlapRatio
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinimumDistanceByDimension
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeatureAsIndividualProportionate
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinFeatureAsIndividual
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MaxOverlapRatio
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumberVoxelsMask
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxels
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatio
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatioMask
calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class HOGFeature
calculate(FeatureCalculationInput<T>) - Method in class AbsoluteValue
calculate(FeatureCalculationInput<T>) - Method in class Divide
calculate(FeatureCalculationInput<T>) - Method in class InvertedMax
calculate(FeatureCalculationInput<T>) - Method in class Multiply
calculate(FeatureCalculationInput<T>) - Method in class IfCondition
calculate(FeatureCalculationInput<T>) - Method in class FromDictionary
calculate(FeatureCalculationInput<T>) - Method in class Maximum
calculate(FeatureCalculationInput<T>) - Method in class Mean
calculate(FeatureCalculationInput<T>) - Method in class MeanGeometric
calculate(FeatureCalculationInput<T>) - Method in class Minimum
calculate(FeatureCalculationInput<T>) - Method in class NormalizedRange
calculate(FeatureCalculationInput<T>) - Method in class Range
calculate(FeatureCalculationInput<T>) - Method in class RangeCompareBase
calculate(FeatureCalculationInput<T>) - Method in class StatisticalBase
calculate(FeatureCalculationInput<T>) - Method in class WithValueBase
calculate(FeatureCalculationInput<T>) - Method in class ConvertUnits
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class EllipsoidBase
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class Ellipticity
calculate(FeatureCalculationInput<FeatureInput>) - Method in class MockFeatureWithCalculation
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class Kernel
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirth
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirthAndKill
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelDeath
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelExchange
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksFromPartition
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksProposed
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksVoxelized
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelMerge
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelReplace
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelSplit
calculateAcceptanceProbability(Kernel<?, ?>, Optional<T>, T, int, KernelCalculationContext) - Method in class AcceptanceProbabilityCalculator
calculateAndOutput(T, FeatureCalculationContext<S>) - Method in class FeatureSource: Processes one input to calculate feature-results and output them to the file-system.
calculateAndOutput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput
calculateAndOutput(MultiInput, FeatureCalculationContext<FeatureTableCalculator<T>>) - Method in class FromObjects
calculateAt(KernelPointCursor) - Method in class AndKernel
calculateAt(KernelPointCursor) - Method in class BinaryKernel: Calculates the boolean at a particular point.
calculateAt(KernelPointCursor) - Method in class ConditionalKernel
calculateAt(KernelPointCursor) - Method in class CountKernel: Calculates the count at a particular point.
calculateAt(KernelPointCursor) - Method in class BinaryKernelMorphological
calculateCheckInitialized(FeatureCalculationInput<T>) - Method in class Feature: Calculates the result of a feature and throws an exception if the feature has not been initialized.
calculateConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
calculateContext(MarkFactoryContext) - Method in class OptimizationContext
calculateCornerMax() - Method in class BoundingBox: The maximum (right-most) point inside the box.
calculateCornerMaxExclusive() - Method in class BoundingBox: The maximum (right-most) point just outside the box.
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelative
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToFirst
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMaxVolume
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMerged
calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToSecond
calculateDensityRatio(double, double, int) - Method in class AnnealScheme
CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CalculateDeriveMarkCollectionInput() - Constructor for class CalculateDeriveMarkCollectionInput
CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CalculateDeriveMarkInput() - Constructor for class CalculateDeriveMarkInput
CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
CalculateDeriveObjectInput(int) - Constructor for class CalculateDeriveObjectInput
CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class CalculateDeriveSingleMemoFromPair
CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateDilationMap(boolean) - Constructor for class CalculateDilationMap
CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateDilationMap
calculateEccentricity(double, double) - Static method in class PrincipalAxisEccentricity
CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
CalculateEllipseLeastSquares() - Constructor for class CalculateEllipseLeastSquares
CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateErosionMap(boolean) - Constructor for class CalculateErosionMap
CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class CalculateErosionMap
calculateFeatureByIdentifier(String, FeatureCalculationInput<T>) - Method in interface FeatureSymbolCalculator: Searches for a feature that matches a particular identifier.
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class ReportFeatureOnObject
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class ReportFeatureOnObjectCollection
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class ReportFeatureOnObjectsBase
CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, FeatureCalculationContext<FeatureTableCalculator<T>>) - Constructor for class CalculateFeaturesForObjects
calculateForAxis(Dimensions, Axis) - Method in class Extent
calculateForAxis(Dimensions, Axis) - Method in class ForSpecificAxis
calculateForAxis(Dimensions, Axis) - Method in class VoxelPhysicalSize
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class FeatureEnergyChannel
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class Intensity
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanMaxSlice
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanShellBase
calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class TextureScore
CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Performs calculations using child-caches instead of the main cache
calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class DotProductOrientationToVector
calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class EllipsoidAxisRatio
calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class EllipsoidMaxAreaIntersectingPlane
calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class FeatureMarkDirection
calculateForNewMark(MarksFromPartition, Set, KernelCalculationContext) - Method in class KernelBirthPartition
calculateForNewMark(T, Set, KernelCalculationContext) - Method in class KernelBirth
calculateForNewMark(VoxelizedMarksWithEnergy, Set, KernelCalculationContext) - Method in class KernelBirthVoxelized
calculateForObjects(ObjectCollectionProvider, LabelsForInput) - Method in class CalculateFeaturesForObjects
calculateForObjects(ObjectCollection, EnergyStack, LabelsForInput) - Method in class CalculateFeaturesForObjects: Calculates the feature-results for objects, and stores the results.
calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShell
calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellBase
calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellMaxSlice
calculateForVoxel(int, int) - Method in class CalculateLevel
calculateForVoxel(int, int) - Method in class CalculateLevelBase
calculateForVoxel(int, int) - Method in class DifferenceCalculateLevelStandardDeviation
calculateFromAllMoments(ImageMoments) - Method in class ImageMomentsBase
calculateFromAllMoments(ImageMoments) - Method in class PrincipalAxisEccentricity
calculateFromAllMoments(ImageMoments) - Method in class RatioPrincipalAxisLength
calculateFromAllMoments(ImageMoments) - Method in class SpecificAxisBase
calculateFromDimensions(Dimensions) - Method in class Area
calculateFromDimensions(Dimensions) - Method in class ForSpecificAxis
calculateFromDimensions(Dimensions) - Method in class FromDimensionsBase
calculateFromDimensions(Dimensions) - Method in class Volume
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisLength
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisOrientation
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class SpecificAxisBase: Calculates the result for the specific moment identified by index
CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
CalculateHistogram(int) - Constructor for class CalculateHistogram
CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation: Calculated a histogram for a specific region on a channel, as identified by a mask in another channel
CalculateHistogramMasked(int, int) - Constructor for class CalculateHistogramMasked
CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateIncrementalOperationMap(boolean) - Constructor for class CalculateIncrementalOperationMap
CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateIncrementalOperationMap
CalculateInputFromDelegate<S,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: A base class for CalculationParts that derive from an existing "delegate" calculation.
CalculateInputFromDelegate(CalculationPart<U, T>, CalculationPartResolver<T>) - Constructor for class CalculateInputFromDelegate
CalculateInputFromDelegate(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegate
CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: Like CalculateInputFromDelegate except assumes optional return value and no parameters.
CalculateInputFromDelegateOption(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegateOption: Creates with a delegate.
CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation: Calculates a single-input from a pair
CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class CalculateInputFromPair
CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.calculation
CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
CalculateIntersecting(ResolvedPart<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class CalculateIntersecting
CalculateLevel - Class in org.anchoranalysis.image.bean.threshold: Calculates a threshold-level from a histogram.
CalculateLevel() - Constructor for class CalculateLevel
calculateLevel(Histogram) - Method in class CalculateLevel: Determines a voxel intensity that can be used for thresholding.
calculateLevel(Histogram) - Method in class CalculateLevelRelativeToThreshold
calculateLevel(Histogram) - Method in class ClampHistogramMax
calculateLevel(Histogram) - Method in class Constant
calculateLevel(Histogram) - Method in class EmptyHistogramConstant
calculateLevel(Histogram) - Method in class Maximum
calculateLevel(Histogram) - Method in class Minimum
calculateLevel(Histogram) - Method in class Otsu
calculateLevel(Histogram) - Method in class OtsuWeighted
calculateLevel(Histogram) - Method in class Quantile
CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
CalculateLevel() - Constructor for class CalculateLevel
CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
CalculateLevelBase() - Constructor for class CalculateLevelBase
calculateLevelIncoming(Histogram) - Method in class CalculateLevelOne
CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
CalculateLevelListBase() - Constructor for class CalculateLevelListBase
CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
CalculateLevelOne() - Constructor for class CalculateLevelOne
CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
CalculateLevelRelativeToThreshold() - Constructor for class CalculateLevelRelativeToThreshold
calculateMaximum() - Method in class Histogram: Calculates the maximum value with non zero-count among the histogram values.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class IntensityMeanCalculator
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class IntensityMeanCalculator
calculateMidpoint(ObjectWithProperties, boolean) - Static method in class Midpoint
calculateMinimum() - Method in class Histogram: Calculates the minimum value with non zero-count among the histogram values.
calculateMinMax(Optional<Resolution>, boolean) - Method in class MarkBounds
calculateMode() - Method in class Histogram: Calculates the mode of the histogram values.
calculateNewMaxCurrentValue() - Method in class PriorityQueueIndexRangeDownhill
CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation
CalculateNumberVoxels(boolean) - Constructor for class CalculateNumberVoxels
CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateObjectMask(CalculateObjectMask) - Constructor for class CalculateObjectMask: Copy constructor
CalculateObjectMask(int, ResolvedPartMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class CalculateObjectMask
calculateOrientation(ObjectWithProperties) - Static method in class Orientation
CalculateOrientationChange - Interface in org.anchoranalysis.image.io.stack: Calculates any needed orientation change.
calculateOrientationChange(Logger) - Method in interface CalculateOrientationChange: Calculates any needed orientation change.
CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlap(int) - Constructor for class CalculateOverlap
CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMask(int, int, byte) - Constructor for class CalculateOverlapMask
CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIP(int) - Constructor for class CalculateOverlapMIP
CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIPBase(int) - Constructor for class CalculateOverlapMIPBase
CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIPRatio(int) - Constructor for class CalculateOverlapMIPRatio
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIP
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPBase
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPRatio
calculatePath() - Method in class MutableDirectory
calculatePath() - Method in class OutputtedFile
calculatePoint(ObjectWithProperties, String) - Static method in class Orientation
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class MergeLists
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class PointsFromOrientationProposer
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class TraversePointsOnContour
calculateResultsForInput(FileInput, FeatureCalculationContext<FeatureList<FeatureInputHistogram>>) - Method in class FromHistogram
calculateResultsForInput(ProvidesStackInput, FeatureCalculationContext<FeatureList<FeatureInputStack>>) - Method in class FromImage
calculateResultsForInput(ImageMetadataInput, FeatureCalculationContext<FeatureList<FeatureInputImageMetadata>>) - Method in class FromImageMetadata
calculateResultsForInput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput: Calculates feature-results for a particular input.
calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class IterateVoxelsMask: Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
calculateScaleFactor(Optional<Dimensions>) - Method in interface ImageSizeSuggestion: Calculates the scaling factor.
CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateShellObjectMask(ResolvedPart<ObjectMask, FeatureInputSingleObject>, ResolvedPart<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class CalculateShellObjectMask
calculateSigma(Dimensions, MessageLogger) - Method in class BlurStrategy
calculateStatisticFrom(Histogram) - Method in class FeatureHistogramStatistic: Calculates the statistic from the histogram, that is subsequently returned as the feature-value.
calculateStatisticFrom(Histogram) - Method in class Mean
calculateStatisticFrom(Histogram) - Method in class CoefficientOfVariation
calculateStatisticFrom(Histogram) - Method in class Count
calculateStatisticFrom(Histogram) - Method in class Kurtosis
calculateStatisticFrom(Histogram) - Method in class Max
calculateStatisticFrom(Histogram) - Method in class MeanRaisedToPower
calculateStatisticFrom(Histogram) - Method in class Median
calculateStatisticFrom(Histogram) - Method in class Min
calculateStatisticFrom(Histogram) - Method in class Mode
calculateStatisticFrom(Histogram) - Method in class NumberDistinctValues
calculateStatisticFrom(Histogram) - Method in class Quantile
calculateStatisticFrom(Histogram) - Method in class Range
calculateStatisticFrom(Histogram) - Method in class RatioNonMode
calculateStatisticFrom(Histogram) - Method in class Skewness
calculateStatisticFrom(Histogram) - Method in class StdDev
calculateStatisticFrom(Histogram) - Method in class Sum
calculateStatisticFrom(Histogram) - Method in class TotalCount
calculateStatisticFrom(Histogram) - Method in class Variance
calculateStatisticFrom(Histogram) - Method in class RatioThreshold
calculateSum() - Method in class Histogram: Calculates the sum of all values in the distribution considering their counts.
calculateSumCubes() - Method in class Histogram: Calculates the cube of the squares of all values in the distribution considering their counts.
calculateSumSquares() - Method in class Histogram: Calculates the sum of the squares of all values in the distribution considering their counts.
calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorMulti: Calculates the results for an input recording the error to an ErrorReporter if anything goes wrong, but throwing no exception.
calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorMultiChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorSingle: Calculates the result for an input recording the error to an ErrorReporter if anything goes wrong, but throwing no exception.
calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleFromMulti
calculateSuppressErrors(T, ErrorReporter) - Method in class SequentialSession: Calculates the next-object in our sequential series, reporting any exceptions into a reporter log
calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class SingleTableCalculator
calculateTemperature(int) - Method in class AnnealScheme
calculateTemperature(int) - Method in class Geometry
calculateTemperature(int) - Method in class NoAnnealing
calculateVolume() - Method in class Dimensions: Calculates the volume of the Extent when considered as a box.
calculateVolume() - Method in class Extent: Calculates the volume of the Extent when considered as a box.
calculateVolumeAsInt() - Method in class Extent: Like Extent.calculateVolume() but uses an int to calculate the volume.
calculateWith(Feature<T>, T, Logger) - Static method in class FeatureSession: Starts a feature-session for a single feature - and performs a calculation.
calculateWithChannel(ObjectMask, Channel) - Method in class CountEqual
calculateWithChannel(ObjectMask, Channel) - Method in class SpecificEnergyChannelBase
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class HasTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxelFaces
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class TouchingVoxels
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberVoxelsAtBorder
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberNeighboringVoxels
calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class OutlineKernelBase
calculateWithResolution(double, Resolution) - Method in class FeatureConvertUnits
calculateWithResolution(double, Resolution) - Method in class WithResolutionBase
calculateWithResolution(double, Resolution) - Method in class UnitsWithinRange
calculateZScore(double, double, double) - Static method in class ZScoreCalculator: Calculates a Z-Score for a particular value and parameterization.
CalculationPart<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.part: A sub-part of the calculation of a feature, that can be cached, and reused by other features.
CalculationPart() - Constructor for class CalculationPart
CalculationPartMap<S,T extends FeatureInput,U,E extends Exception> - Class in org.anchoranalysis.feature.calculate.part: Similar to a CalculationPart but stores several evaluation results, differentiated by a key.
CalculationPartMap(int) - Constructor for class CalculationPartMap: Creates for a particular cache-size.
CalculationPartResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.part: Searches a cache to reuses a CalculationPart if it already exists.
calculationResultsNeeded(MultiLevelOutputEnabled) - Method in class FeatureOutputNames: If any output is enabled that requires calculation of feature results?
calculator() - Method in interface FeatureCalculationCache: A means of calculating feature values using this cache.
calculatorForAll(FeatureList<T>) - Method in class FeatureCalculatorFromProvider: Calculates all image-features in the feature-store
calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class FeatureCalculatorFromProvider: Calculates a single-feature that comes from a provider (but can reference the other features from the store)
call(CheckedSupplier<T, E>) - Method in class CachedSupplierBase: Gets the value supplied by supplier via the cache if it exists, or otherwise via the supplier.
call() - Method in class CallableJob
CallableJob<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.task.processor: A job derived from a Task that can be placed on different threads
CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class CallableJob: Constructor.
callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class IterateVoxelsNeighbors: Iterate over each point in the neighborhood of an existing point.
canEqual(Object) - Method in class DoubleList
canEqual(Object) - Method in class DoubleSet
canEqual(Object) - Method in class IntegerList
canEqual(Object) - Method in class IntegerSet
canEqual(Object) - Method in class StringList
canEqual(Object) - Method in class StringSet
canEqual(Object) - Method in class RootPath
canEqual(Object) - Method in class EqualToBean
canEqual(Object) - Method in class GreaterThanBean
canEqual(Object) - Method in class GreaterThanEqualToBean
canEqual(Object) - Method in class LessThanBean
canEqual(Object) - Method in class LessThanEqualToBean
canEqual(Object) - Method in class RelationBean
canEqual(Object) - Method in class RelationToConstant
canEqual(Object) - Method in class Indexable
canEqual(Object) - Method in class ChildCacheName
canEqual(Object) - Method in class FeatureInputDimensions
canEqual(Object) - Method in class FeatureInputEnergy
canEqual(Object) - Method in class FeatureInputNull
canEqual(Object) - Method in class SimpleName
canEqual(Object) - Method in class SizeXY
canEqual(Object) - Method in class CalculateLevelOne
canEqual(Object) - Method in class BinaryNotOffVoxels
canEqual(Object) - Method in class BinaryNotOnVoxels
canEqual(Object) - Method in class BinaryOffVoxels
canEqual(Object) - Method in class BinaryOnVoxels
canEqual(Object) - Method in class BinaryVoxelsBase
canEqual(Object) - Method in class CalculateInputFromPair
canEqual(Object) - Method in class CalculateNumberVoxels
canEqual(Object) - Method in class FeatureInputImageMetadata
canEqual(Object) - Method in class FeatureInputObjectCollection
canEqual(Object) - Method in class FeatureInputPairObjects
canEqual(Object) - Method in class FeatureInputSingleObject
canEqual(Object) - Method in class FeatureInputStack
canEqual(Object) - Method in class UnsignedBuffer
canEqual(Object) - Method in class UnsignedBufferAsInt
canEqual(Object) - Method in class UnsignedByteBuffer
canEqual(Object) - Method in class UnsignedIntBuffer
canEqual(Object) - Method in class UnsignedShortBuffer
canEqual(Object) - Method in class QuadraticEquationSolver.QuadraticRoots
canEqual(Object) - Method in class MeanScale
canEqual(Object) - Method in class RegionMap
canEqual(Object) - Method in class RegionMembership
canEqual(Object) - Method in class RegionMembershipWithFlags
canEqual(Object) - Method in class CalculateDeriveSingleMemoFromPair
canEqual(Object) - Method in class FeatureInputMark
canEqual(Object) - Method in class IndexableMarksWithEnergy
canEqual(Object) - Method in class FeatureInputAllMemo
canEqual(Object) - Method in class FeatureInputPairMemo
canEqual(Object) - Method in class FeatureInputSingleMemo
canEqual(Object) - Method in class MemoList
canEqual(Object) - Method in class ColoredMarksWithDisplayStack
canEqual(Object) - Method in class MarksWithDisplayStack
canEqual(Object) - Method in class OverlayMark
canEqual(Object) - Method in class FeedbackBeginParameters
canEqual(Object) - Method in class IndexableOverlays
canEqual(Object) - Method in class AxisLimits
canEqual(Object) - Method in class CalculateLevelListBase
canEqual(Object) - Method in class CalculateLevelRelativeToThreshold
canEqual(Object) - Method in class ClampHistogramMax
canEqual(Object) - Method in class Constant
canEqual(Object) - Method in class EmptyHistogramConstant
canEqual(Object) - Method in class IfGreaterThan
canEqual(Object) - Method in class IfLessThan
canEqual(Object) - Method in class Maximum
canEqual(Object) - Method in class Minimum
canEqual(Object) - Method in class Otsu
canEqual(Object) - Method in class OtsuWeighted
canEqual(Object) - Method in class Quantile
canEqual(Object) - Method in class MorphologicalIterations
canEqual(Object) - Method in class CalculateIntersecting
canEqual(Object) - Method in class CalculateDeriveObjectInput
canEqual(Object) - Method in class CalculateInputFromDelegate
canEqual(Object) - Method in class CalculateInputFromDelegateOption
canEqual(Object) - Method in class CalculateIncrementalOperationMap
canEqual(Object) - Method in class CalculateObjectMask
canEqual(Object) - Method in class CalculateShellObjectMask
canEqual(Object) - Method in class CalculateDilation
canEqual(Object) - Method in class CalculateDilationMap
canEqual(Object) - Method in class CalculateErosion
canEqual(Object) - Method in class CalculateErosionMap
canEqual(Object) - Method in class CalculateHistogram
canEqual(Object) - Method in class CalculateHistogramMasked
canEqual(Object) - Method in class ChangeableOutputSequence
canEqual(Object) - Method in class SortedSetChannel
canEqual(Object) - Method in class SortedSetSlice
canEqual(Object) - Method in class AllSlicesMaskEverythingNonZero
canEqual(Object) - Method in class AllSlicesMaskNonZero
canEqual(Object) - Method in class CenterSlice
canEqual(Object) - Method in class CenterSliceBase
canEqual(Object) - Method in class CenterSliceWindow
canEqual(Object) - Method in class GreatestAreaSlice
canEqual(Object) - Method in class IndexedRegionBase
canEqual(Object) - Method in class SelectSlicesBase
canEqual(Object) - Method in class SelectSlicesWithIndexBase
canEqual(Object) - Method in class Specific
canEqual(Object) - Method in class CalculateDeriveMarkCollectionInput
canEqual(Object) - Method in class CalculateDeriveMarkInput
canEqual(Object) - Method in class CalculateOverlap
canEqual(Object) - Method in class CalculateOverlapMask
canEqual(Object) - Method in class CalculateOverlapMIP
canEqual(Object) - Method in class CalculateOverlapMIPBase
canEqual(Object) - Method in class CalculateOverlapMIPRatio
canEqual(Object) - Method in class HOGParameters
canEqual(Object) - Method in class FitResult
canEqual(Object) - Method in class CalculateEllipseLeastSquares
canEqual(Object) - Method in class CalculateEllipsoidLeastSquares
canEqual(Object) - Method in class Orientation2D
canEqual(Object) - Method in class Orientation3DEulerAngles
canEqual(Object) - Method in class OrientationAxisAngle
canEqual(Object) - Method in class OrientationRotationMatrix
canEqual(Object) - Method in class Point3d
canEqual(Object) - Method in class Point3f
canEqual(Object) - Method in class Point3i
canEqual(Object) - Method in class Tuple3d
canEqual(Object) - Method in class Tuple3f
canEqual(Object) - Method in class Tuple3i
canEqual(Object) - Method in class Vector3d
canExceptionBeCombined(Throwable) - Method in exception BeanMisconfiguredXMLException
canExceptionBeCombined(Throwable) - Method in exception LocalisedBeanException
canExceptionBeCombined(Throwable) - Method in exception AnchorCombinableException: Can another exception be combined with this exception?
canExceptionBeCombined(Throwable) - Method in exception NamedProviderGetException
canExceptionBeSkipped(Throwable) - Method in exception BeanMisconfiguredXMLException
canExceptionBeSkipped(Throwable) - Method in exception LocalisedBeanException
canExceptionBeSkipped(Throwable) - Method in exception AnchorCombinableException: Can another exception be skipped, when we combine with the current exception?
canExceptionBeSkipped(Throwable) - Method in exception NamedProviderGetException
canValueRangeChange() - Method in class Interpolator: Returns true if it's possible for values to be created after interpolation that aren't found in the input-image.
canValueRangeChange() - Method in class InterpolatorImgLib2Lanczos
canValueRangeChange() - Method in class InterpolatorImgLib2Linear
canValueRangeChange() - Method in class InterpolatorImgLib2NearestNeighbor
canValueRangeChange() - Method in class InterpolatorNone
canValueRangeChange() - Method in class InterpolatorRecordExecutionTime
canValueRangeChange() - Method in class InterpolatorImageJ
canValueRangeChange() - Method in class InterpolatorOpenCV
capacity() - Method in class UnsignedBuffer: The capacity of the buffer ala Buffer.capacity.
capacity() - Method in class VoxelBuffer: The capacity (i.e.
capacity() - Method in class VoxelBufferUnsigned
castAs() - Method in class Feature: Casts the feature to having a different input-type.
Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
Cell() - Constructor for class Cell
CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
CenterOfGravity(Axis) - Constructor for class CenterOfGravity: Creates for a specific axis.
CenterOfGravity() - Constructor for class CenterOfGravity
centerOfGravity() - Method in class ObjectMask: Calculates center-of-gravity across all axes.
centerOfGravity(Axis) - Method in class ObjectMask: Calculates center-of-gravity for one specific axis only.
centerOfGravity() - Method in class BoundingBox: A mid-point in the bounding-box, corresponding to the mean of all points inside the box.
CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
CenterOnMask() - Constructor for class CenterOnMask
centerPoint() - Method in class Mark
centerPoint() - Method in class MarkWithPosition
centerPoint() - Method in class LineSegment
centerPoint() - Method in class PointList
centerPoint() - Method in class Polygon
centerPoint() - Method in class PolygonCurve
centerPoint() - Method in class EllipseStandardFormConverter
CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
CenterSlice() - Constructor for class CenterSlice
CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
CenterSliceBase() - Constructor for class CenterSliceBase
CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region: Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one slice, specifically centerSlice+- windowSize
CenterSliceWindow() - Constructor for class CenterSliceWindow
chainCode(int, int, int) - Static method in class ChainCodesDirection
chainCodes(int) - Method in class WatershedEncoding: Decodes a chain-code into a point
ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Maps directions to chain codes
ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
ChangeableOutputSequence() - Constructor for class ChangeableOutputSequence
changedMarkIDArray() - Method in class Kernel: The mark ids that were changed in the last energy calculation for the kernel
changedMarkIDArray() - Method in class KernelBirth
changedMarkIDArray() - Method in class KernelBirthAndKill
changedMarkIDArray() - Method in class KernelDeath
changedMarkIDArray() - Method in class KernelExchange
changedMarkIDArray() - Method in class KernelInitialMarksFromPartition
changedMarkIDArray() - Method in class KernelInitialMarksProposed
changedMarkIDArray() - Method in class KernelInitialMarksVoxelized
changedMarkIDArray() - Method in class KernelMerge
changedMarkIDArray() - Method in class KernelReplace
changedMarkIDArray() - Method in class KernelSplit
changedOffset(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Calculates the offset in the buffer for a voxel, indicated by its relative-change in position.
changeExtension(Path, NonImageFileFormat, FileFormat) - Static method in class FormatExtensions: Change the extension in a path.
changeExtent(Extent) - Method in class BoundingBox: Creates a copied BoundingBox but with a different extent.
changeExtentZ(int) - Method in class BoundingBox: Creates a copied BoundingBox but with a different extent in the Z-dimension.
changeInput(U) - Method in class InputBound: Immutably changes the input-object
changeInputAndSharedState(U, V) - Method in class InputBound: Immutably changes the input-object and shared-state
changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class IterateVoxelsAll: Changes each voxel, reading and writing the buffer as an int.
changePrefix(DirectoryWithPrefix) - Method in class OutputterTarget: Creates a new OutputterTarget with a changed prefix.
changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class OutputterChecked: Creates a OutputterChecked with a changed prefix and WriteOperationRecorder.
changeZ(int, int) - Method in class BoundingBox: Creates a copied BoundingBox but with a different corner and extent in the Z-dimension.
Channel - Class in org.anchoranalysis.image.core.channel: A channel from an image.
Channel(Voxels<?>, Optional<Resolution>) - Constructor for class Channel: Creates for particular voxels and resolution.
channel() - Method in class Mask: The underlying channel which contains the binary-values.
channel(String) - Static method in class ReferenceFactory
ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert: Base class to convert Channels from one type to another specific type.
ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class ChannelConverter
ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached: A channel-converter that has been permanently associated with a particular object.
ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert: Converts a channel from one voxel data-type to one of multiple other types.
ChannelConverterMulti() - Constructor for class ChannelConverterMulti
ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a channel(s) at a particular timepoint into a stack(s).
ChannelConvertStyle() - Constructor for class ChannelConvertStyle
ChannelEntry - Class in org.anchoranalysis.image.io.bean.channel
ChannelEntry(String, int) - Constructor for class ChannelEntry
ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel corresponding to one of several data-types.
ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type FloatVoxelType.
ChannelFactoryFloat() - Constructor for class ChannelFactoryFloat: Default constructor.
ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel for a specific data-type.
ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class ChannelFactorySingleType
ChannelFactoryUnsignedByte - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedByteVoxelType.
ChannelFactoryUnsignedByte() - Constructor for class ChannelFactoryUnsignedByte: Default constructor.
ChannelFactoryUnsignedInt - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedIntVoxelType.
ChannelFactoryUnsignedInt() - Constructor for class ChannelFactoryUnsignedInt: Default constructor.
ChannelFactoryUnsignedShort - Class in org.anchoranalysis.image.core.channel.factory: Creates a Channel with voxel-type UnsignedShortVoxelType.
ChannelFactoryUnsignedShort() - Constructor for class ChannelFactoryUnsignedShort: Default constructor.
ChannelFilter - Class in org.anchoranalysis.image.io.bean.channel: Applies a filter to a particular channel
ChannelFilter() - Constructor for class ChannelFilter
ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output: Writes a single channel to a file.
ChannelGenerator(String) - Constructor for class ChannelGenerator
ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input
ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack
ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class ChannelGetterForTimepoint
ChannelMap - Class in org.anchoranalysis.image.io.bean.channel
ChannelMap() - Constructor for class ChannelMap
ChannelMapper - Class in org.anchoranalysis.image.core.stack: Helps retrieve channel and an associated converter and apply operation on them jointly.
ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class ChannelMapper
channelNames() - Method in interface NamedChannelsForSeries
channelNames() - Method in class NamedChannelsForSeriesConcatenate
channelNames() - Method in class NamedChannelsForSeriesMap
channelNames(Logger) - Method in interface OpenedImageFile: The names of each channel, if they are known.
channelNames(Logger) - Method in class OpenedMultiFile
ChannelProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Channel and associated Stack.
ChannelProvider() - Constructor for class ChannelProvider
ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider: A channel-provider based-on two input channel-providers that must be of the same dimensionality
ChannelProviderBinary() - Constructor for class ChannelProviderBinary
ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
ChannelProviderTernary() - Constructor for class ChannelProviderTernary
ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
ChannelProviderUnary() - Constructor for class ChannelProviderUnary
channels() - Method in class ImageInitialization
ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped: Source of channels for aggregating.
ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class ChannelSource
channelsPerByteArray(IFormatReader) - Method in class Default
channelsPerByteArray(IFormatReader) - Method in class ForceChannelsPerByteArray
channelsPerByteArray(IFormatReader) - Method in class ReadOptions: The number of channels returned with each call to IFormatReader.openBytes(int).
channelsPerByteArray(IFormatReader) - Method in class ReadOptionsDelegate
check(Mark, RegionMap, EnergyStack) - Method in class CheckMark: Checks a mark
check(Channel, Mask) - Static method in class DimensionsChecker
check(Channel, String, Dimensions) - Static method in class DimensionsChecker: Checks a channel to make sure it's the same size as an an existing channel
check(Mask, String, Dimensions) - Static method in class DimensionsChecker: Checks a channel to make sure it's the same size as an an existing channel
check(Mark, RegionMap, EnergyStack) - Method in class AndList
check(Mark, RegionMap, EnergyStack) - Method in class AnySliceCenterOnMask
check(Mark, RegionMap, EnergyStack) - Method in class CenterOnMask
check(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
check(Mark, RegionMap, EnergyStack) - Method in class Not
check(Mark, RegionMap, EnergyStack) - Method in class RadiiMinRatio
check(Mark, RegionMap, EnergyStack) - Method in class VolumeMin
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Check() - Constructor for class Check
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
Check() - Constructor for class Check
check(T) - Static method in class BeanTestChecker: Checks if a bean has all necessary items, throwing a run-time exception if it does not.
checkAbsolutePath() - Method in class OutputPrefixerSettings
checkAndInit(T, P, Logger) - Static method in class BeanTestChecker: Checks if a bean has all necessary items as with BeanTestChecker.check(T) and also initializes the bean.
CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.cache.finder: For particular child-caches, check if a session-input is available from another LRU-cache and reuse.
CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class CheckCacheForSpecificChildren
checkChannelType(VoxelDataType) - Method in class ConsistentChannelChecker: Checks that a channel has the same type (max value) as the others
checkCompatibleWith(Mark) - Method in class KernelProposer
CheckedBiConsumer<S,T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BiConsumer but can also throw a checked exception.
CheckedBiFunction<S,T,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BiFunction but can also throw a checked exception.
CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BooleanSupplier but can also throw an exception.
CheckedConsumer<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Consumes a value and throws an exception.
CheckedFunction<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Function but can also thrown an exception.
CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Consumes an int and throws an exception.
CheckedIntFunction<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like IntFunction but can also thrown an exception.
CheckedPredicate<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Predicate but can also throw an exception.
CheckedProgressingSupplier<R,E extends Exception> - Interface in org.anchoranalysis.core.progress: Like CheckedSupplier but can update a progress-reporter as the operation progresses.
CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Runnable but can also throw an exception.
CheckedStream - Class in org.anchoranalysis.core.functional: Map operations for streams that can throw checked-exceptions.
CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional: An exception that wraps another exception, but exposes itself as a RuntimeException.
CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Supplier but can also throw an exception.
CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like ToDoubleBiFunction but can also thrown an exception.
CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like ToIntFunction but can also thrown an exception.
CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like a UnaryOperator but allows an exception to be thrown.
CheckedUnsupportedOperationException - Exception in org.anchoranalysis.core.exception: When a particular operation is unsupported in particular circumstances.
CheckedUnsupportedOperationException() - Constructor for exception CheckedUnsupportedOperationException: Creates with a default message indicating that the operation is unsupported.
CheckedUnsupportedOperationException(String) - Constructor for exception CheckedUnsupportedOperationException: Creates with a message explaining that the operation is unsupported.
CheckException - Exception in org.anchoranalysis.mpp.feature.error
CheckException(String) - Constructor for exception CheckException
CheckException(String, Throwable) - Constructor for exception CheckException
CheckException(Throwable) - Constructor for exception CheckException
checkExtentMatch(BoundingBox, BoundingBox) - Static method in class ExtentMatchHelper: Checks that the Extents of two bounding boxes are identical.
checkIdenticalDataType(VoxelDataType) - Method in class VoxelsUntyped: Do the voxels have a data-type that is equal to match?
CheckIfAllowed - Class in org.anchoranalysis.io.output.writer: Only allows outputs, if the output-name is allowed in the OutputterChecked.
CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class CheckIfAllowed
checkIfConnected() - Method in class ObjectMask: Determines if an object-mask is connected.
CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark: A predicate on a mark to check if a condition has been satisfied.
CheckMark() - Constructor for class CheckMark
CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
CheckMarkWithMask() - Constructor for class CheckMarkWithMask
checkMisconfigured(BeanInstanceMap) - Method in class AnchorBean: Checks that a bean's properties conform to expectations.
CheckMisconfigured - Class in org.anchoranalysis.bean.initializable: Routines for checking that particular patterns exist with bean-properties.
checkMisconfigured(BeanInstanceMap) - Method in class SequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class FeatureEvaluator
checkMisconfigured(BeanInstanceMap) - Method in class OutputWriteSettings
checkMisconfigured(BeanInstanceMap) - Method in interface FeedbackReceiver
checkMisconfigured(BeanInstanceMap) - Method in class FromStack
checkMisconfigured(BeanInstanceMap) - Method in class ExtractSliceRange
checkMisconfigured(BeanInstanceMap) - Method in class Erode
checkMisconfigured(BeanInstanceMap) - Method in class Sequence
checkMisconfigured(BeanInstanceMap) - Method in class ThreeChannels
checkMisconfigured(BeanInstanceMap) - Method in class ThreeColoredObjects
checkMisconfigured(BeanInstanceMap) - Method in class FromChannelOrMask
checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeature
checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeatureSequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class Intersection
checkMisconfigured(BeanInstanceMap) - Method in class IntensityMeanShellBase
checkMisconfigured(BeanInstanceMap) - Method in class LastDirectories
checkMisconfigured(BeanInstanceMap) - Method in class CoupledManifestsInputManager
checkMisconfigured(BeanInstanceMap) - Method in class HOGFeature
checkMisconfigured(BeanInstanceMap) - Method in class FromDictionary
checkMisconfigured(BeanInstanceMap) - Method in class QuickExperiment
checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetExperiment
checkMisconfigured(BeanInstanceMap) - Method in class MultiInputManagerQuick
checkMisconfigured(BeanInstanceMap) - Method in class NamedChannelsQuick
checkMisconfigured(BeanInstanceMap) - Method in class ExperimentResultsExperimentStructure
checkMisconfigured(BeanInstanceMap) - Method in class ExperimentStructure
checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetStructuredExperiment
CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
CheckParsedFilePathBag() - Constructor for class CheckParsedFilePathBag
checkResultVector(ResultsVector) - Static method in class ConstantsInListFixture: checks that a result-vector has the results we expect from the feature-list associated with this fixture
checkSize(Extent) - Method in class HOGParameters: Throws an exception if an image of size extent cannot be described by these parameters.
checkUnsupported3D(Channel) - Static method in class SegmentChannelIntoObjects
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class SegmentChannelIntoObjects
checkUnsupportedSeeds(Optional<ObjectCollection>) - Static method in class SegmentChannelIntoObjects
ChildCacheFinder - Interface in org.anchoranalysis.feature.session.cache.finder: Strategy to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface FeatureCalculationCache: Gets/creates a child-cache for a given name.
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class CheckCacheForSpecificChildren
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in interface ChildCacheFinder: Selects a child-cache given a parent and a child-name.
childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class DefaultChildCacheFinder
ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache: A unique identifier for a child-cache's name commposed potentially of two elements.
ChildCacheName(Class<?>) - Constructor for class ChildCacheName: Uses only the class as an identifier.
ChildCacheName(Class<?>, int) - Constructor for class ChildCacheName: Uses only the class combines with an integer part-name.
ChildCacheName(Class<?>, String) - Constructor for class ChildCacheName: Uses both the class and a part-name as an identifier.
children() - Method in class ErrorNodeImpl
ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
ChooseOneList() - Constructor for class ChooseOneList
Circle - Class in org.anchoranalysis.mpp.mark.conic: A circle
Circle(Bound) - Constructor for class Circle: Creates with a radius within particular bounds.
Circle(Circle) - Constructor for class Circle: Copy constructor
Circle() - Constructor for class Circle
circleAt(Point2i, double) - Static method in class CircleObjectFixture
CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
circumference(int) - Method in class Ellipse
clamp(Point3i, Dimensions) - Static method in class PointClamper
clamp(Point3d, Dimensions) - Static method in class PointClamper
ClampHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
ClampHistogramMax() - Constructor for class ClampHistogramMax
clampTo(Extent) - Method in class BoundingBox: Ensures that the box fits inside a Extent by reducing any values to their limits in the respective dimension.
classificationString(boolean) - Static method in class BinaryOutcomeImageLabeller
classInCurrentJar() - Method in class LauncherConfig: A class which we use to determine the base location for pathRelativeProperties.
clean() - Method in class VoxelizedMarksWithEnergy
clean() - Method in class EnergyMemoList
cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByChannel
cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByRegion
cleanUp(VoxelPartitionFactory<T>) - Method in interface VoxelPartition
cleanUp(VoxelPartitionFactory<Histogram>) - Method in class VoxelPartitionHistogram
cleanUp() - Method in interface VoxelizedMark
clear() - Method in class FeatureList: Removes all of the elements from this list.
clear() - Method in class UnsignedBuffer: Clears the buffer ala Buffer.clear().
clear() - Method in class UpdatableMarksList
clearBest() - Method in class DualState
clipTo(T, Extent) - Method in interface AccessObjectMask: Ensures the element lies within a certain extent.
clipTo(ObjectMask, Extent) - Method in class AccessObjectMaskSimple
clipTo(Extent) - Method in class ObjectMask: Makes sure an object fits inside an extent, removing any parts which do not.
close() - Method in interface Progress: Ends tracking progress, to be called after any calls to Progress.update(int).
close() - Method in class ProgressConsole
close() - Method in class ProgressIgnore
close() - Method in class ProgressIncrement: Ends tracking progress, to be called after any calls to ProgressIncrement.update().
close() - Method in class ProgressMultiple
close(boolean, boolean) - Method in class StatefulNullMessageLogger
close(boolean, boolean) - Method in class ConsoleMessageLogger
close(boolean, boolean) - Method in class FailureOnlyMessageLogger
close(boolean, boolean) - Method in class MessageLoggerList
close(boolean, boolean) - Method in interface StatefulMessageLogger
close(boolean, boolean) - Method in class TextFileMessageLogger
close() - Method in class FeatureCSVWriter: Closes any open file-handles.
close() - Method in interface OpenedImageFile: Closes the opened image-file, removing any intermediate data-structures.
close() - Method in class CSVWriter
close() - Method in class CSVReader.OpenedCSVFile
close() - Method in class ReadByLine: Closes any opened-files
close(ErrorReporter) - Method in interface InputFromManager: Performs all tidying up, file-closing etc.
close(ErrorReporter) - Method in class InputFromManagerDelegate
close(ErrorReporter) - Method in class MultiInput
close(ErrorReporter) - Method in class StackWithMap
close() - Method in class SharedStateFilteredImageOutput
close() - Method in class SharedStateSelectedSlice
close() - Method in class OpenedMultiFile
close() - Method in class OnnxModel
close() - Method in class OpenCVModel
closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterCreator>, InputOutputContext) - Method in class FeatureExporter: Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
closeAndWriteOutputs(ExportFeaturesStyle) - Method in class SharedStateSegmentInstance: Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
closeAnyOpenIO() - Method in class FeatureResultsAndThumbnails: Closes any open IO and removes redundant structures stored in memory.
closeLogger() - Method in class RecordingCounter: Closes the logger.
ClusterByTimestamp - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Associates particular timestamp with each file, and clusters.
ClusterByTimestamp() - Constructor for class ClusterByTimestamp
clusterFor(File) - Method in class ClusterMembership: Finds the corresponding cluster for a particular file.
ClusterIdentifier - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Uniquely identifies a cluster.
ClusterIdentifier(ZoneOffset) - Constructor for class ClusterIdentifier: Creates with no name.
ClusterIdentifier(String, ZoneOffset) - Constructor for class ClusterIdentifier: Creates with a constant-name.
ClusterMembership - Class in org.anchoranalysis.plugin.io.file.copy: A mapping of files to membership of particular clusters.
ClusterMembership(ClusterIdentifier) - Constructor for class ClusterMembership
CODE_MINIMA - Static variable in class WatershedEncoding
CODE_PLATEAU - Static variable in class WatershedEncoding
CODE_TEMPORARY - Static variable in class WatershedEncoding
CODE_UNVISITED - Static variable in class WatershedEncoding
CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CoefficientOfVarianceFromAll() - Constructor for class CoefficientOfVarianceFromAll
coefficientOfVariation(Histogram) - Static method in class HistogramStatistics: Calculates the coefficient-of-variation of a distribution of values, represented by their histogram.
CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the coefficient of variation of all the values in the histogram.
CoefficientOfVariation() - Constructor for class CoefficientOfVariation
CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive: Removes the file-name from a path, but keeps the directories and preserves the file-extension.
CollapseFileName() - Constructor for class CollapseFileName
CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection: Writes a collection of elements as a subdirectory with each element as a single file in the subdirectory.
CollectionGenerator(Generator<T>, String) - Constructor for class CollectionGenerator
collectResult() - Method in interface ProcessChangedPointAbsoluteMasked: Collects the result of the operation after processing neighbor voxels.
collectResult() - Method in interface ProcessVoxelNeighbor: Collects the result of the operation after processing neighbor pixels.
collectResult() - Method in interface ProcessVoxelNeighborAbsolute: Collects the result of the operation after processing neighbor voxels.
colorAxis(Axis) - Method in class PlotColorScheme
colorChart(JFreeChart) - Method in class PlotColorScheme
ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB stack into another color space using OpenCV.
ColorConverterBase() - Constructor for class ColorConverterBase
ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Base class for providers that draw entities (an outline or filled) on a background
ColoredBase() - Constructor for class ColoredBase
ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Like ColoredBase but uses a generator to determine the colors for the objects
ColoredBaseWithGenerator() - Constructor for class ColoredBaseWithGenerator
ColoredMarks - Class in org.anchoranalysis.mpp.mark
ColoredMarks() - Constructor for class ColoredMarks
ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter) - Constructor for class ColoredMarks
ColoredMarks(Mark, RGBColor) - Constructor for class ColoredMarks
ColoredMarks(MarkCollection, ColorList) - Constructor for class ColoredMarks
ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider: Draws a colored representation (outline or filled) of an MarkCollection on a background
ColoredMarks() - Constructor for class ColoredMarks
ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter) - Constructor for class ColoredMarksWithDisplayStack
ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class ColoredMarksWithDisplayStack
ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of a ObjectMask on a background
ColoredMask() - Constructor for class ColoredMask
ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object: Associates a ColorList with a ObjectCollection
ColoredObjectCollection() - Constructor for class ColoredObjectCollection: Create with an empty collection.
ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class ColoredObjectCollection: Create with a single object and color.
ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class ColoredObjectCollection: Create with an existing object and color list.
ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of an ObjectCollection on a background
ColoredObjects() - Constructor for class ColoredObjects
coloredObjectsToDraw(Dimensions) - Method in class ColoredBase: Creates colored-objects to be drawn.
coloredObjectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
coloredObjectsToDraw(Dimensions) - Method in class ColoredMask
coloredObjectsToDraw(Dimensions) - Method in class ThreeColoredObjects
ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
ColoredOverlayCollection() - Constructor for class ColoredOverlayCollection
ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class ColoredOverlayCollection
colorFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes: A color for a particular object
colorForEachIndex(int) - Method in class ColorScheme: Assigns a color to each index value from a list of size numberColors.
ColorIndex - Interface in org.anchoranalysis.core.color: Associates an RGB-color with each index.
ColorIndexModulo - Class in org.anchoranalysis.core.color: Derives a new ColorIndex from an existing ColorIndex applying a modulo operation to each index call.
ColorIndexModulo(ColorIndex) - Constructor for class ColorIndexModulo
colorLegend(LegendTitle) - Method in class PlotColorScheme
ColorList - Class in org.anchoranalysis.core.color: A list of colors, each corresponding to a particular index position.
ColorList(Color...) - Constructor for class ColorList: Create for one or more colors of type Color.
ColorList(RGBColor...) - Constructor for class ColorList: Create for one or more colors of type RGBColor.
ColorList() - Constructor for class ColorList
colorPlot(XYPlot) - Method in class PlotColorScheme
colorPlot(CategoryPlot) - Method in class PlotColorScheme
ColorProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a ColorList.
ColorProvider() - Constructor for class ColorProvider
ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a sequence of related colors.
ColorScheme() - Constructor for class ColorScheme
ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme: Like ColorScheme but employs a unary operator on a call to an existing ColorScheme.
ColorSchemeUnary() - Constructor for class ColorSchemeUnary
ColorSchemeUnary(ColorScheme) - Constructor for class ColorSchemeUnary
colorSpaceCode() - Method in class ColorConverterBase: The color space conversion code to use from OpenCV, that defines the color-space to convert to.
colorSpaceCode() - Method in class ConvertRGBToHSV
colorSpaceCode() - Method in class ConvertRGBToLab
column(int) - Method in class RotationMatrix: Extracts a column from the rotation-matrix as a point.
ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
ColumnDefinition() - Constructor for class ColumnDefinition
combine(List<PermutationAssigner>) - Static method in class PermutationAssignerFactory: Combines multiple existing assigners into a single PermutationAssigners.
Combine - Class in org.anchoranalysis.image.io.bean.object.draw
Combine() - Constructor for class Combine
Combine(List<DrawObject>) - Constructor for class Combine
combine(boolean, boolean) - Method in class MultiLevelAnd
combine(boolean, boolean) - Method in class MultiLevelBinary
combine(boolean, boolean) - Method in class MultiLevelOr
combine(boolean, boolean) - Method in class SingleLevelAnd
combine(boolean, boolean) - Method in class SingleLevelBinary
combine(boolean, boolean) - Method in class SingleLevelOr
Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
Combine() - Constructor for class Combine
CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
CombineBase() - Constructor for class CombineBase
CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task: Combines multiple CSV files into a single CSV file.
CombineCSV() - Constructor for class CombineCSV
combined() - Method in class PathDifference: The directory-component (if it exists) and filename-component combined.
combined() - Method in class SplitPath: A path that combines the root together with the remainder.
combineDescription(String, String) - Method in class AddConstantTo
combineDescription(String, String) - Method in class ConstantToThePowerOf
combineDescription(String, String) - Method in class DivideByConstant
combineDescription(String, String) - Method in class MultiplyByConstant
combineDescription(String, String) - Method in class SubtractFrom
combineDescription(String, String) - Method in class ToThePowerOfConstant
combineDescription(String, String) - Method in class ReplaceUnusualValue
combineDescription(String, String) - Method in class WithValueBase
combineDescriptionsRecursively(String, String) - Method in exception AnchorCombinableException: Traverses through a set of nested-exceptions creating a description for each "combined" exception, and combining them into a single string.
CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined: Several generators combined together with a common element-type.
CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class CombinedListGenerator
CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class CombinedListGenerator
CombinedListGenerator(Generator<T>...) - Constructor for class CombinedListGenerator
CombinedListGenerator() - Constructor for class CombinedListGenerator
CombinedName - Class in org.anchoranalysis.feature.io.name: A name which is unique when a primaryName is combined with a secondaryName
CombinedName(String, String) - Constructor for class CombinedName: Creates with explicit strings for both parts.
CombineObjectsForFeatures<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: A way to combine (or not combine) objects so that they provide a feature-table.
CombineObjectsForFeatures() - Constructor for class CombineObjectsForFeatures
CombineRasterGenerator<T> - Class in org.anchoranalysis.image.io.bean.stack.combine: Combines a number of generators of Raster images by tiling their outputs together
CombineRasterGenerator() - Constructor for class CombineRasterGenerator
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelAnd
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelBinary
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelOr
CombineToOnePath - Class in org.anchoranalysis.plugin.mpp.contour.path.merge
combineToOnePath(List<ContiguousVoxelPath>) - Static method in class CombineToOnePath: Combines all the contiguous paths to a single-path.
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype: Calculates which VoxelDataType to use when combining two other voxel-data types, but without losing precision.
combineTypes(VoxelDataType, VoxelDataType) - Static method in class CombineTypes: What data-type to use to represent voxels of both type1 and type2?
combineValueAndFeature(double, double) - Method in class AddConstantTo
combineValueAndFeature(double, double) - Method in class ConstantToThePowerOf
combineValueAndFeature(double, double) - Method in class DivideByConstant
combineValueAndFeature(double, double) - Method in class MultiplyByConstant
combineValueAndFeature(double, double) - Method in class SubtractFrom
combineValueAndFeature(double, double) - Method in class ToThePowerOfConstant
combineValueAndFeature(double, double) - Method in class ReplaceUnusualValue
combineValueAndFeature(double, double) - Method in class WithValueBase
combineWithSuffix(String) - Method in class FilenameSplitExtension: Inserts a suffix after the base-name, but before the extension, immutably.
CommandLineException - Exception in org.anchoranalysis.launcher: An exception thrown at run-time while processing command-line args
CommandLineException(String) - Constructor for exception CommandLineException
CommandLineExtracter - Class in org.anchoranalysis.launcher.options: Adds methods to CommandLine for querying and extracting options, with and without arguments.
CommandLineExtracter(CommandLine) - Constructor for class CommandLineExtracter
CommandLineOptions - Class in org.anchoranalysis.launcher.options: All command-line options used by the launcher.
common() - Method in class InitializationContext
common() - Method in interface InputOutputContext: Creates a CommonContext a context that contains a subset of this context.
CommonContext - Class in org.anchoranalysis.core.log: A logger with additional configuration that are coupled together widely in the code
CommonContext(Logger, Path) - Constructor for class CommonContext
CommonPath - Class in org.anchoranalysis.core.system.path: Finds the common root directory of a set of paths.
commonType(Stream<VoxelDataType>) - Static method in class FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} of a stream of types.
commonType(VoxelDataType, VoxelDataType) - Static method in class FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} both first and second.
ComparableSource - Class in org.anchoranalysis.annotation.io.bean.comparer: A set of elements, loaded from the file-system, to be compared to another set.
ComparableSource() - Constructor for class ComparableSource
Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point: Imposes an ordering on any sub-type of Tuple3d.
Comparator3d() - Constructor for class Comparator3d
Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point: Imposes an ordering on any sub-type of Tuple3i.
Comparator3i() - Constructor for class Comparator3i
ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name: Orders two name-values by their name (alphabetic order from standard String.compareTo(String).
ComparatorOrderByName() - Constructor for class ComparatorOrderByName
compare(NameValue<V>, NameValue<V>) - Method in class ComparatorOrderByName
compare(T, T) - Method in class Comparator3d
compare(T, T) - Method in class Comparator3i
CompareAnnotations<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison: Task to compare a set of annotations to a segmentation or another set of annotations.
CompareAnnotations() - Constructor for class CompareAnnotations
compareTo(AssociatedIndex) - Method in class Indexable
compareTo(MultiName) - Method in class CombinedName
compareTo(MultiName) - Method in class SimpleName
compareTo(EigenvalueAndVector) - Method in class EigenvalueAndVector
compareTo(SortedSetChannel) - Method in class SortedSetChannel
compareTo(SortedSetSlice) - Method in class SortedSetSlice
compareTo(BoundingBox) - Method in class BoundingBox: Exposed via ReadableTuple3i to keep it read-only
compareTo(Extent) - Method in class Extent
compareTo(ReadableTuple3i) - Method in interface ReadableTuple3i
CompareWithRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Compares a value with a range, returning specified constants if its inside the range, below it or above it
CompareWithRange() - Constructor for class CompareWithRange
CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Like CompareWithRange but uses features to calculate boundary values
CompareWithRangeFeature() - Constructor for class CompareWithRangeFeature
CompareXML - Class in org.anchoranalysis.test: Compares two XML documents to see if they are equal.
comparison() - Method in interface ImageCounterWithStatistics: Creates statistics from counted images and the payload T passed for annotated images.
ComparisonSharedState<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
ComparisonSharedState(CSVAssignment, int, Function<String, ImageCounterWithStatistics<T>>) - Constructor for class ComparisonSharedState
CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
completeProjection() - Method in interface ProjectableBuffer: Performs any final operation before turning the projected buffer.
Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer: Combines a transformation from S to U with one from U to T
Compose() - Constructor for class Compose
Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class Compose
CompressAnyTIFF - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a Bytewise copy.
CompressAnyTIFF() - Constructor for class CompressAnyTIFF
computeIfAbsent(K) - Method in class MapCreate: Gets an existing element from the map, newly creating and storing the element if it's absent.
computeInitialFeasibleSolution() - Method in class HungarianAlgorithm: Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
Concatenate - Class in org.anchoranalysis.bean.define.adder: Concatenates a list of adders.
Concatenate() - Constructor for class Concatenate
Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider: Combines one or more ColorProviders into a unitary ColorProvider.
Concatenate() - Constructor for class Concatenate
Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
Concatenate() - Constructor for class Concatenate
Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Combines all the channels from one or more sources (stacks, channels etc.)
Concatenate() - Constructor for class Concatenate
Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Concatenates the inputs from multiple InputManagers that all provide the same input-type.
Concatenate() - Constructor for class Concatenate
ConcatenateFileTypes - Class in org.anchoranalysis.io.generator: Concatenates the arrays of FileType that may be returned from write operations.
ConcatenateFileTypes() - Constructor for class ConcatenateFileTypes: Creates to always use a list for tracking.
ConcatenateFileTypes(boolean) - Constructor for class ConcatenateFileTypes: Create to use a list for tracking if a flag is true, otherwise to just remember the last result of each call to ConcatenateFileTypes.add(org.anchoranalysis.io.manifest.file.FileType[]).
ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
ConcurrentJobMonitor(long) - Constructor for class ConcurrentJobMonitor
ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel: Executes another BinaryKernel iff a predicate is satisfied for a particular point.
ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class ConditionalKernel: Creates with a particular delegate BinaryKernel and a predicate that tests each point.
ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats: Singleton class for making sure Bioformats is configured configured.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteDivideByParam
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFirstSecondOrder
ConicBase - Class in org.anchoranalysis.mpp.mark.conic
ConicBase() - Constructor for class ConicBase
ConicBase(MarkWithPosition) - Constructor for class ConicBase
ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
ConicFitterBase() - Constructor for class ConicFitterBase
ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Performs a binary-segmentation of the channel and converts its connected-components into objects
ConnectedComponentsFromBinarySegmentation() - Constructor for class ConnectedComponentsFromBinarySegmentation
ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Converts a binary-mask into its connected components
ConnectedComponentsFromMask() - Constructor for class ConnectedComponentsFromMask
considerVisit(Point3i, int, ObjectMask) - Method in class VisitScheduler
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerAnd
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerConvexAboutRoot
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerMaxDistanceAlongContour
considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerUniformSample
ConsiderVisit - Interface in org.anchoranalysis.plugin.mpp.contour: Whether to visit a point or not.
ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped: Checks that the histograms created from channels all have the same data type, res, max-value etc.
ConsistentChannelChecker() - Constructor for class ConsistentChannelChecker
ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ConsoleAccepted() - Constructor for class ConsoleAccepted
ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ConsoleAggregatedReporter(double) - Constructor for class ConsoleAggregatedReporter
ConsoleAggregatedReporter() - Constructor for class ConsoleAggregatedReporter
ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
ConsoleMessageLogger() - Constructor for class ConsoleMessageLogger
Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A constant value that is entirely invariant to the feature-input.
Constant(double) - Constructor for class Constant: Constructor with a particular value.
Constant(String, double) - Constructor for class Constant: Constructor with a particular value and a custom-name.
Constant() - Constructor for class Constant
Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: A constant value for thresholding.
Constant() - Constructor for class Constant
Constant(int) - Constructor for class Constant
Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive: Always generates a constant path irrespective of the the input
Constant() - Constructor for class Constant
Constant(String) - Constructor for class Constant
Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
Constant() - Constructor for class Constant
ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale
ConstantScaleFactor() - Constructor for class ConstantScaleFactor
ConstantsInListFixture - Class in org.anchoranalysis.test.feature
ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
ConstantToThePowerOf() - Constructor for class ConstantToThePowerOf
ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight: All marks have weight of 1
ConstantWeight() - Constructor for class ConstantWeight
consumeChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class ChannelMapper: Like ChannelMapper.mapChannelIfSupported(int, BiFunction, Function) but the mapping has no return-type.
containerOptional() - Method in class WithContainerBase
containerRequired() - Method in class WithContainerBase
contains(Double) - Method in class DoubleList
contains(Double) - Method in class DoubleSet
contains(Integer) - Method in class IntegerList
contains(Integer) - Method in class IntegerSet
contains(T) - Method in interface PrimitiveBeanCollection: Whether the collection contains a particular element?
contains(String) - Method in class StringList
contains(String) - Method in class StringSet
contains(ChildCacheName) - Method in class CacheTransferSourceCollection
contains(Feature<FeatureInput>) - Method in class SharedFeatures: Whether a particular feature is contained in this instance.
contains(Point3d) - Method in class Dimensions: Is a point of type Point3d contained within the extent?
contains(Point3i) - Method in class Dimensions: Is a point of type ReadableTuple3i contained within the Extent?
contains(BoundingBox) - Method in class Dimensions: Is box entirely contained within the extent?
contains(Point3i) - Method in class IntersectingObjects: All elements that contain a particular point.
contains(Point3i) - Method in class ObjectMask: Whether a particular point exists within the object-mask?
contains(double) - Method in class ResolvedBound
contains(Object) - Method in class UpdatableMarksList
contains(Object) - Method in class MarkCollection
contains() - Method in class BoundingBox: For evaluating whether this bounding-box contains other points, boxes etc.?
contains(Point2i) - Method in class Extent: Is a point of type Point2i contained within the extent in the XY plane?
contains(Point3d) - Method in class Extent: Is a point of type Point3d contained within the extent?
contains(ReadableTuple3i) - Method in class Extent: Is a point of type ReadableTuple3i contained within the extent?
contains(int, int, int) - Method in class Extent: Is a point contained within the extent?
contains(BoundingBox) - Method in class Extent: Is box entirely contained within the extent?
contains(ReadableTuple3i) - Method in class BoundingBoxRTree: Which objects contain a particular point?
contains(double) - Method in class IntervalRTree: Which objects contain a particular point?
containsAll(Collection<?>) - Method in class UpdatableMarksList
containsChild(ChildCacheName) - Method in class CacheTransferSource
containsEdge(V, V) - Method in class GraphWithoutPayload: Does the graph contain a particular edge?
containsEdge(V, V) - Method in class GraphWithPayload: Does the graph contain a particular edge?
containsFamily(Class<?>) - Method in class BeanInstanceMap: Is a particular family-type contained in the map?
containsKey(String) - Method in class Dictionary: Does a parameter exist with a particular key?
containsMark(Mark) - Method in class RandomCollectionWithAddCriteria
containsOrEmpty() - Method in class DebugModeParameters
containsStream(ReadableTuple3i) - Method in class BoundingBoxRTree: Like BoundingBoxRTree.contains(org.anchoranalysis.spatial.point.ReadableTuple3i) but returns a Stream instead of a Set.
containsStream(double) - Method in class IntervalRTree: Like IntervalRTree.contains(double) but returns a Stream instead of a Set.
containsStream(Point) - Method in class RTree: Which objects contain a particular point?
containsVertex(V) - Method in class GraphWithoutPayload: Does the graph contain a particular vertex?
containsVertex(V) - Method in class GraphWithPayload: Does the graph contain a particular vertex?
containsX(double) - Method in class Extent: Is a value contained within the extent on the X-axis?
containsX(int) - Method in class Extent: Is a value contained within the extent on the X-axis?
containsY(double) - Method in class Extent: Is a value contained within the extent on the Y-axis?
containsY(int) - Method in class Extent: Is a value contained within the extent on the Y-axis?
containsZ(double) - Method in class Extent: Is a value contained within the extent on the Z-axis?
containsZ(int) - Method in class Extent: Is a value contained within the extent on the Z-axis?
ContiguousVoxelPath - Class in org.anchoranalysis.plugin.mpp.contour.path: A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
ContiguousVoxelPath(Point3i, Point3i) - Constructor for class ContiguousVoxelPath: With a single initial-point, and maybe a connection point
ContiguousVoxelPath() - Constructor for class ContiguousVoxelPath: Without any connection-point
continueFurther(int, double, int, MessageLogger) - Method in class TerminationCondition: Whether to continue for an additional iteration step or not.
continueFurther(int, double, int, MessageLogger) - Method in class TerminationConditionListOr
continueFurther(int, double, int, MessageLogger) - Method in class TriggerTerminationCondition
continueFurther(int, double, int, MessageLogger) - Method in class NumberIterations
continueFurther(int, double, int, MessageLogger) - Method in class UnchangedBase
Contour - Class in org.anchoranalysis.spatial.point: A path of successively-neighbored points.
Contour() - Constructor for class Contour
contoursForObject(ObjectMask) - Static method in class CVFindContours: Calculates the extreme outer contours from an ObjectMask as OpenCV defines contours.
ContourTraverser - Class in org.anchoranalysis.plugin.mpp.contour: Iteratively moves around a ObjectMask that describes the contour of an object.
ContourTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class ContourTraverser
ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert: The different ways of converting the voxel-data-type in a Channel.
convert(Channel, ConversionPolicy) - Method in class MaxIntensity
convert(Channel, ConversionPolicy) - Method in interface ChannelConverterAttached: Converts the voxel-type in a Channel.
convert(Channel, ConversionPolicy) - Method in class MaxIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class QuantileIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class UpperLowerQuantileIntensityFromHistogram
convert(Stack, ConversionPolicy) - Method in class ChannelConverter: Like ChannelConverter.convert(Channel, ConversionPolicy) but converts every channel in a Stack.
convert(Channel, ConversionPolicy) - Method in class ChannelConverter: Converts channel to have voxels with data-type T.
convert(Channel, VoxelDataType) - Method in class ChannelConverterMulti: Converts a Channel's voxels to another type.
convert(DisplayStack) - Static method in class ConvertDisplayStackToRGB
convert(ByteBuffer, int, OrientationChange, boolean) - Method in class ConvertTo
convert(ByteBuffer, int, OrientationChange, boolean) - Method in class UnsignedByteFromUnsignedByte
convert(Mark) - Method in class MarkToObjectConverter: Converts a Mark to an equivalent ObjectMask.
Convert<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel by applying a converter (no histogram is involved in the conversion).
Convert() - Constructor for class Convert
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class ChannelConvertStyle: Converts a particular set of channels.
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class IndependentChannels
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class RGB
convert(int) - Method in class NumberToStringConverter: Converts number to a string, padding with leading zeros if necessary to ensure the desired width.
convert2iTo3d(List<Point2i>) - Static method in class PointConverter: Convert a list of Point2i to a list of Point3d.
convert2iTo3f(List<Point2i>) - Static method in class PointConverter: Convert a list of Point2i to a list of Point3f.
convert3dTo3f(List<Point3d>) - Static method in class PointConverter: Convert a list of Point3d to a list of Point3f.
convert3fTo3d(List<Point3f>) - Static method in class PointConverter: Convert a list of Point3f to a list of Point3d.
convert3i(List<Point3f>, boolean) - Static method in class PointConverter: Convert a list of Point3f to a list of Point3i, optionally rounding values.
convert3i(List<Point3d>) - Static method in class PointConverter: Convert a list of Point3d to a list of Point3i.
convert3iTo3f(List<Point3i>) - Static method in class PointConverter: Convert a list of Point3i to a list of Point3f.
ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
ConvertBase() - Constructor for class ConvertBase
convertBeforeAssign(DisplayStack) - Method in class DisplayStackGenerator
convertBeforeAssign(Stack) - Method in class FlattenStackGenerator
convertBeforeAssign(T) - Method in class RasterGeneratorBridge
convertBeforeAssign(T) - Method in class RasterGeneratorDelegateToRaster: Converts an element before setting it on the delegate.
convertBeforeTransform(Stack) - Method in class DisplayStackGenerator
convertBeforeTransform(Stack) - Method in class FlattenStackGenerator
convertBeforeTransform(Stack) - Method in class RasterGeneratorBridge
convertBeforeTransform(Stack) - Method in class RasterGeneratorDelegateToRaster: Converts an element before calling RasterGeneratorDelegateToRaster.transform(T) on the delegate.
ConvertChannelTo<T> - Class in org.anchoranalysis.image.bean.channel.converter: Converts a channel from one type to another.
ConvertChannelTo() - Constructor for class ConvertChannelTo
ConvertChannelToWithHistogram<T> - Class in org.anchoranalysis.image.bean.channel.converter: Creates a ChannelConverterAttached<Histogram, T> for converting a channel to a particular type, making use of a Histogram.
ConvertChannelToWithHistogram() - Constructor for class ConvertChannelToWithHistogram
convertCode(int, int, EncodedVoxels, Point3i) - Method in class EncodedIntBuffer: Convert code to connected-component
convertCropped(DisplayStack, BoundingBox) - Static method in class ConvertDisplayStackToRGB
ConvertDisplayStackToRGB - Class in org.anchoranalysis.image.io.stack
ConvertedInput - Class in org.anchoranalysis.plugin.mpp.experiment.shared: A converted-input, together with any logged messages associated with it.
ConvertedInput(U, StringBuilder) - Constructor for class ConvertedInput
ConvertedToRuntimeException(Throwable) - Constructor for exception CheckedStream.ConvertedToRuntimeException: Creates for any exception.
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, FloatBuffer) - Method in class ToFloatNoScaling
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, T) - Method in class VoxelsConverter: Copies a value from the current position in a FloatBuffer to the current position in a buffer of type T.
convertFrom(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class VoxelsConverter: Creates a new voxels of type T and copies the voxels from from.
ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert: Converts an ImagePlus into a channel or voxels.
ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert: Convert from the OpenCV Mat to a Stack.
ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical: converts a feature to a physical distance in a XY place that is isometric
ConvertFromPhysicalVolume() - Constructor for class ConvertFromPhysicalVolume
convertFromUnits(double, String) - Static method in class SpatialUnits: Converts a value from another unit-type to base units.
convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits: Converts a value from another unit-type to base units.
ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format: Converts each input-image to an output format, optionally changing the bit depth.
ConvertImageFormat() - Constructor for class ConvertImageFormat
ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.convert: Converts NamedChannelsInput to a variety of others to match a delegate task.
ConvertNamedChannels() - Constructor for class ConvertNamedChannels
ConvertNamedChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: An input object that converts NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsInputToStack(NamedChannelsInput) - Constructor for class ConvertNamedChannelsInputToStack: Create with an input.
ConvertNamedChannelsInputToStack(NamedChannelsInput, int, Optional<String>) - Constructor for class ConvertNamedChannelsInputToStack: Create with an input.
ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: Manager that converts (one channel) NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsToStack() - Constructor for class ConvertNamedChannelsToStack
ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB image to the HSV color space.
ConvertRGBToHSV() - Constructor for class ConvertRGBToHSV
ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.color: Converts a RGB image to the Lab color space.
ConvertRGBToLab() - Constructor for class ConvertRGBToLab
convertSliceOfSingleChannel(ByteBuffer, int, OrientationChange) - Method in class ConvertTo: Converts a slice of single-channel into a newly created VoxelBuffer.
ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert: Converts a subset of raw voxel bytes in a buffer to a possibly a buffer with different data-type.
ConvertTo(Function<VoxelsUntyped, Voxels<T>>, IntFunction<T>, Function<T, VoxelBuffer<T>>) - Constructor for class ConvertTo
convertTo3d(Point2d) - Static method in class PointConverter: Convert a Point2d to a Point3d using 0 as the value of the Z-axis component.
convertTo3i(Point2i) - Static method in class PointConverter: Convert a Point2i to a Point3i using 0 as the value of the Z-axis component.
convertTo3i(Point2i, int) - Static method in class PointConverter: Convert a Point3i to a Point2i using an explicit value for the Z-axis component.
ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert: Converts a channel or voxels into a ImagePlus.
ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert: Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor.
ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the Img used in ImgLib2.
ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert: Converts common image data-structures used by Anchor to the Mat class used by OpenCV.
ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the NativeImg used in ImgLib2.
convertToObjects(Dimensions) - Method in interface AnnotationWithMarks: Creates an object-collection that is a voxelized representation of the marks in the annotation.
convertToOutputType(Channel) - Method in class GradientBase
convertToPhysical(double, UnitConverter) - Method in class ConvertFromPhysicalVolume
convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalAreaXY
convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalDistance
convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalVolume
convertToPhysical(double, UnitConverter) - Method in class FeatureConvertUnits
ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
ConvertToPhysicalAreaXY() - Constructor for class ConvertToPhysicalAreaXY
ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class ConvertToPhysicalDistance
ConvertToPhysicalDistance() - Constructor for class ConvertToPhysicalDistance
ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical: converts a feature to a physical distance in a XY place that is isometric
ConvertToPhysicalVolume() - Constructor for class ConvertToPhysicalVolume
convertToString(Path) - Static method in class PathOperations: Converts a path to a string, making sure it uses UNIX-style separators.
convertToUnits(double, String) - Static method in class SpatialUnits: Converts a value in base-units to another unit-type.
convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits: Converts a value in base-units to another unit-type.
ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert: Converts a ImageProcessor to a voxel-buffer of particular data-type.
ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
ConvertUnits() - Constructor for class ConvertUnits
convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class ToByte
convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class ToFloatNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
convertUnsignedByte(UnsignedByteBuffer, T) - Method in class VoxelsConverter: Copies a value from the current position in a UnsignedByteBuffer to the current position in a buffer of type T.
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class ToFloatNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
convertUnsignedInt(UnsignedIntBuffer, T) - Method in class VoxelsConverter: Copies a value from the current position in a UnsignedIntBuffer to the current position in a buffer of type T.
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class ToFloatNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
convertUnsignedShort(UnsignedShortBuffer, T) - Method in class VoxelsConverter: Copies a value from the current position in a UnsignedShortBuffer to the current position in a buffer of type T.
convertValue(short) - Method in class ToUnsignedShort
convertValue(short) - Method in class UnsignedShortFromSignedShort
convertValue(short) - Method in class UnsignedShortFromUnsignedShort
ConvertWithHistogram<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel to a different voxel data-type by applying a converter with an associated histogram.
ConvertWithHistogram() - Constructor for class ConvertWithHistogram
ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.convexhull: Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
ConvexHull2D() - Constructor for class ConvexHull2D
convexHull2D(List<Point2i>) - Static method in class ConvexHullUtilities: Like ConvexHullUtilities.convexHull2D(List, int) but uses a default minimum number of points.
convexHull2D(List<Point2i>, int) - Static method in class ConvexHullUtilities: Apply a convex-hull algorithm to filter a set of points.
ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.convexhull
ConvexHull3D() - Constructor for class ConvexHull3D
ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.convexhull
ConvexHullBase() - Constructor for class ConvexHullBase
ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, ImageFileEncoding, OrientationChange) - Method in class ConvertTo: Copies the channels in the source buffer into a particular DestinationChannelForIndex.
copyAllFrames(IFormatReader, List<Channel>, Progress, ImageFileShape, ConvertTo<?>, ReadOptions, OrientationChange) - Static method in class CopyConvert: Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way.
copyChange(MarkCollection) - Method in class MarksFromPartition: Makes a copy, with different marks
copyChangeDictionary(Dictionary) - Method in class EnergyStack: Makes a copy of the EnergyStack but assigns a new Dictionary.
copyChangeIterationsDilation(int) - Method in class MorphologicalIterations: Copies the bean setting an new value for iterationsDilation
copyChangeOrientation(ByteBuffer, boolean, int, T, OrientationChange) - Method in class ConvertTo: Copy the bytes, changing orientation.
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class ToUnsignedByteWithScaling
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromFloat
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromUnsignedByteInterleaving
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class FloatFromUnsignedByte
copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class FloatFromUnsignedInt
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer, OrientationChange) - Method in class UnsignedIntFromUnsignedInt
copyChangeOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer, OrientationChange) - Method in class ToUnsignedShort
CopyContext<T> - Class in org.anchoranalysis.plugin.io.input.path: Context parameters when copying many files from a source directory to a destination directory.
CopyContext(Path, Path, T) - Constructor for class CopyContext
CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert: Copies the bytes from a IFormatReader to a list of channels, converting if necessary.
CopyFiles<T> - Class in org.anchoranalysis.plugin.io.bean.task: Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.
CopyFiles() - Constructor for class CopyFiles
CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: A method used for copying files (e.g.
CopyFilesMethod() - Constructor for class CopyFilesMethod
CopyFilesNaming<T> - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: How an output name (and path) is selected for an input file when copying.
CopyFilesNaming() - Constructor for class CopyFilesNaming
CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
CopyFilesNamingOne() - Constructor for class CopyFilesNamingOne
CopyFilesNamingWithoutSharedState - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Base class for implementations of CopyFilesNaming where each file is copied independently of the others.
CopyFilesNamingWithoutSharedState() - Constructor for class CopyFilesNamingWithoutSharedState
copyFrom(int, int, ResultsVector, int) - Method in class ResultsVector: Copies a contiguous subset of results from another vector.
copyFrom(VoxelsUntyped, Voxels<T>) - Method in class VoxelsConverter: Copies voxels from a source (of any type) to voxels of type T.
copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class VoxelsConverter: Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class VoxelsConverter: Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class VoxelsConverter: Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class VoxelsConverter: Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
copyInit(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine: Copies objects of a particular class from the define AND initializes
copyKeepOrientation(ByteBuffer, boolean, int, T) - Method in class ConvertTo: Copy the bytes, without changing orientation.
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class ToUnsignedByteWithScaling
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromFloat
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromUnsignedByteInterleaving
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class FloatFromUnsignedByte
copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class FloatFromUnsignedInt
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer) - Method in class UnsignedIntFromUnsignedInt
copyKeepOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer) - Method in class ToUnsignedShort
copyObjectsFrom(NamedProvider<ObjectCollection>) - Method in class ImageInitialization
copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class DisplayStack: Copies pixels from a particular channel to an output buffer.
copyProvider(Class<?>, NamedProviderStore<T>) - Method in class PopulateStoreFromDefine: Copies objects of a particular class from the define AND initializes as a provider
copyStacksFrom(NamedProvider<Stack>) - Method in class ImageInitialization
copyTo(SharedObjects, Logger) - Method in interface ExportSharedObjects: Adds any exported shared-objects to sharedObjects.
copyTo(SharedObjects, Logger) - Method in class MultiInput
copyTo(SharedObjects, Logger) - Method in class FromCSVInput
copyToDirectory(File) - Method in class TestLoader: Copies all the data in the test-data folder (recursively), preserving file modification times.
copyToDirectory(String[], File) - Method in class TestLoader: Copies specific subdirectories from the test-data folder (recursively), preserving file modification times.
copyVoxelFrom(int, VoxelBuffer<T>, int) - Method in class VoxelBuffer: Copies one particular intensity-value from another VoxelBuffer into this buffer.
copyVoxelsTo(BoundingBox, VoxelsUntyped, BoundingBox) - Method in class VoxelsUntyped: Copies the voxels into a destination, but only those voxels inside a bounding-box.
copyVoxelsTo(ObjectMask, VoxelsUntyped, BoundingBox) - Method in class VoxelsUntyped: Copies the voxels into a destination, but only those voxels inside an ObjectMask.
copyWithoutInit(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine: Copies objects of a particular class from the define WITHOUT doing any initialization
cornerMin() - Method in class BoundedVoxels: The minimum corner of the bounding box in each dimension.
cornerMin() - Method in class BoundingBox: The minimum corner of the bounding box in each dimension.
correctedEndIndex(int) - Method in class IndexRangeNegative: The end-index, maybe corrected so that it is no longer negative.
correctedStartIndex(int) - Method in class IndexRangeNegative: The start-index, maybe corrected so that it is no longer negative.
CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment: Stores costs between all possible pairings between elements from two lists.
CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
CostOverlapWithinMidpointDistance() - Constructor for class CostOverlapWithinMidpointDistance
Count - Class in org.anchoranalysis.feature.bean.results: The number of the results from a particular feature.
Count() - Constructor for class Count
count() - Method in class PredicateAtCorner
count() - Method in class PredicateImplementation
count() - Method in interface VoxelsPredicate: Counts the number of values satisfying the predicate - across all voxels.
count(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>) - Method in class CountIntersectingVoxels
Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Counts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)
Count() - Constructor for class Count
countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded: Counts all voxels in the intersection of two bounded-voxels of type BoundedVoxels that match a predicate.
countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded: Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
CountEqual() - Constructor for class CountEqual
Counter - Class in org.anchoranalysis.math.arithmetic: A simple counter that increments.
Counter() - Constructor for class Counter
countForObject(ObjectMask) - Method in class PredicateAtCorner
countForObject(ObjectMask) - Method in class PredicateImplementation
countForObject(ObjectMask) - Method in interface VoxelsPredicate: Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.
countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class CountVoxelsIntersectingObjects: Counts the number of intersecting-voxels between two object-masks.
countIntersectingVoxels(ObjectMask) - Method in class ObjectMask: Counts the number of intersecting-voxels between two object-masks.
CountIntersectingVoxels - Class in org.anchoranalysis.mpp.overlap: Counts the number of intersecting-pixels where bytes are encoded as region memberships
CountIntersectingVoxels(byte) - Constructor for class CountIntersectingVoxels
CountIntersectingVoxels(PredicateRegionMembership) - Constructor for class CountIntersectingVoxels
countIntersectingVoxels() - Method in class MaxIntensityProjectionPair
CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count: Base class for kernels that return a count (positive integer) for every voxel.
CountKernel() - Constructor for class CountKernel: Creates with a kernel-size of three.
CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count: For every voxel on the outline, count all neighbors that are adjacent.
CountKernelNeighborhood() - Constructor for class CountKernelNeighborhood
CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count: The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an ObjectMask.
CountKernelNeighborhoodMask(ObjectMask) - Constructor for class CountKernelNeighborhoodMask: Create with object-mask.
countMasked(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, byte) - Method in class CountIntersectingVoxels
countMatching(IntPredicate) - Method in class Histogram: Gets the total count of all values that match a predicate.
countOff() - Method in class BinaryVoxels: Counts the number of voxels with an off state.
countOn() - Method in class BinaryVoxels: Counts the number of voxels with an on state.
countThreshold(RelationToThreshold) - Method in interface VoxelStatistics: Counts the number of voxels that exist, relative to a threshold.
countThreshold(RelationToThreshold) - Method in class VoxelStatisticsCombined
countThreshold(RelationToThreshold) - Method in class VoxelStatisticsFromHistogram
CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but counts voxels matching a predicate rather than iterating.
CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like CountVoxelsIntersectingBounded but specifically counts areas of intersection between two ObjectMasks.
countXY() - Method in class RunningSumPoint: The count for the X or Y dimensions.
countZ() - Method in class RunningSumPoint: The count for the Z dimension.
CoupledManifests - Class in org.anchoranalysis.plugin.io.manifest
CoupledManifests(DeserializedManifest, int, Logger) - Constructor for class CoupledManifests
CoupledManifests(Manifest, DeserializedManifest, Logger) - Constructor for class CoupledManifests
CoupledManifestsInputManager - Class in org.anchoranalysis.plugin.io.bean.input.manifest
CoupledManifestsInputManager() - Constructor for class CoupledManifestsInputManager
create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class CostMatrix: Creates by calculating the cost between elements.
create(Provider<T>) - Static method in class OptionalProviderFactory: Creates from a provider if non-null.
create() - Method in class RandomNumberGeneratorBean: Creates the RandomNumberGenerator.
create() - Method in class EqualToBean
create() - Method in class GreaterThanBean
create() - Method in class GreaterThanEqualToBean
create() - Method in class LessThanBean
create() - Method in class LessThanEqualToBean
create() - Method in class RelationBean: Creates a DoubleBiPredicate that implements the relation.
create() - Method in class StringMap: Derives a Map representation for the mapping.
create(boolean, T) - Static method in class OptionalFactory: Creates only if a boolean flag is true, otherwise returns Optional.empty().
create(boolean, Supplier<T>) - Static method in class OptionalFactory: Creates only if a boolean flag is true, otherwise returns Optional.empty().
create(String) - Static method in class OptionalFactory: Creates Optional.empty() for an empty string, or otherwise Optional.of().
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class LoggingDestination: Creates a logger for this destination
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class OnlyIf
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class SwitchDetailedLogging
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToConsole
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToMultiple
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFile
create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFileOnlyIfFailure
create(boolean) - Static method in class ExecutionTimeRecorderFactory: Creates either a ExecutionTimeRecorder that records times, or ignores the recording depending on whether any output is enabled that needs the execution-time.
create(Class<? extends FeatureInput>) - Method in interface CacheCreator: Creates a FeatureCalculationCache that accepts a particular input type.
create(SharedObjects) - Static method in class FeatureRelatedInitialization: Creates with shared-objects, and otherwise empty initialization.
create(Logger, Path) - Static method in class FeatureRelatedInitialization: Creates a log and a model-directory, and otherwise empty initialization.
create(FeatureCSVMetadata, Outputter, boolean) - Static method in class FeatureCSVWriter: Maybe creates a FeatureCSVWriter depending if the output is allowed.
create(Optional<String>, String) - Static method in class MultiNameFactory: Creates either a multi-name that is either has a single part or a double part.
create(FeatureOutputMetadata, FeatureCSVWriterCreator, boolean) - Static method in class FeatureCalculationResultsFactory: Creates with appropriate support classes for outputting.
create(FeatureCSVMetadata) - Method in interface FeatureCSVWriterCreator: Maybe creates a FeatureCSVWriter corresponding to particular metadata.
create(Class<? extends FeatureInput>) - Method in class HorizontalCacheCreator
create() - Method in class ImgLib2Lanczos
create() - Method in class ImgLib2Linear
create() - Method in class InterpolatorBean
create() - Method in class None
create(Stack) - Static method in class BufferedImageFromStack: Creates a BufferedImage from a Stack.
create(Dimensions, VoxelDataType) - Method in class ChannelFactory: Creates an empty initialized channel for a particular data-type.
create(Voxels<?>) - Method in class ChannelFactory: Create a Channel from particular voxels.
create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactory: Create a Channel from particular voxels.
create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactorySingleType: Create a Channel from voxels and a resolution.
create(String) - Static method in class ImageSizeSuggestionFactory: Creates a suggestion for how to resize an image.
create(Map<Integer, T>, UnaryOperator<T>) - Method in class DecodeLabels: Creates a map of elements to other elements that are labelled with unique integers (sequentially increasing) in voxels.
create(int) - Method in class DecodeLabels: Creates a list of elements from voxels that are labelled with unique integers (sequentially increasing).
create(Collection<Point3i>) - Static method in class ObjectFromPointsFactory: Create an ObjectMask from a collection of points.
create(Channel) - Static method in class DisplayStack: Creates from a Channel.
create(Stack) - Static method in class DisplayStack: Creates from a RGBStack.
create(RGBStack) - Static method in class DisplayStack: Creates from a RGBStack.
create(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class InitializationFactory
create(InputOutputContext) - Static method in class ImageInitializationFactory
create(InputOutputContext, Optional<ImageSizeSuggestion>) - Static method in class ImageInitializationFactory
create() - Static method in class RasterDirectoryObjectsGenerator
create(SliceBufferIndex<T>) - Method in interface VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with buffers from SliceBufferIndex.
create(ObjectCollection, Extent, boolean, boolean) - Static method in class NeighborGraph: Create the graph with object-masks as vertices, where edges represent the number of neighboring voxels between objects.
create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class NeighborGraph: Like NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a list of elements which form the vertices.
create(ObjectCollection) - Static method in class IntersectingObjects: Creates from an ObjectCollection.
create(IFormatReader, VoxelDataType, int) - Static method in class ConvertToFactory
create(Path) - Static method in class CSVWriter: Creates and starts a CSVWriter (it's always allowed, so will never return null)
create(String, Optional<ManifestDescription>, OutputterChecked, String) - Static method in class TextFileOutputter: Creates a TextFileOutput.
create() - Method in class InterpolatorBeanImageJ
create(InputManagerParameters) - Method in class FilesProvider: Creates or provides a list of files.
create(InputManagerParameters) - Method in class FilesProviderUnary
create(InputManagerParameters) - Method in class FilesProviderWithDirectory
create(InputManagerParameters) - Method in class SpecificPathList
create(Optional<MultiLevelOutputEnabled>) - Method in class AddToDefaults
create(Optional<MultiLevelOutputEnabled>) - Method in class IgnoreUnderscorePrefixUnless
create(Optional<MultiLevelOutputEnabled>) - Method in class NoneExcept
create(Optional<MultiLevelOutputEnabled>) - Method in class OutputEnabledRules: Creates rules for determining whether an output is enabled or disabled.
create(Optional<MultiLevelOutputEnabled>) - Method in class Permissive
create(Optional<MultiLevelOutputEnabled>) - Method in class PermissiveExcept
create(CommandLine, Path, Path) - Static method in class ExperimentExecutorFactory: Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument
create() - Method in class MarkEllipseFactory
create() - Method in class MarkEllipsoidFactory
create() - Method in class MarkFactory
create() - Method in class MarkPointListFactory
create() - Method in class EnergySchemeCreator
create() - Method in class EnergySchemeCreatorByElement
create(EnergyStackWithoutParameters) - Method in class DictionaryForImageCreator
create(int) - Method in interface VoxelPartitionFactory
create(int) - Method in class VoxelPartitonFactoryHistogram
create(ImageInitialization, SharedObjects) - Static method in class PointsInitialization
create(Optional<? extends ExportSharedObjects>, InitializationContext, Optional<Define>) - Static method in class MarksInitializationFactory
create(List<Point3d>) - Static method in class PointListFactory
create(List<Point3d>, int) - Static method in class PointListFactory
create(IntToFloatFunction, Point2i) - Static method in class RotatableBoundingBoxFactory: Builds a bounding-box from the 5-element floating-point vector returned from the EAST algorithm.
create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class PxlMarkMemoFactory
create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class VoxelizedMarkFactory
create(Mark) - Method in class ProposerContext
create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class Plot: Creates a graph
create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class LinePlot
create(InputManagerParameters) - Method in class FromAnnotations
create() - Method in interface PermuteFirstSecondOrder.CreateFirstSecondOrder
create(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, FeatureOutputNames, FeatureExporterContext) - Static method in class FeatureExporter: Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.
create(NamedFeatureStore<T>, LabelHeaders, FeatureOutputNames, FeatureExporterContext) - Static method in class FeatureExporter: Alternative static constructor that creates a shared-state from a NamedFeatureStore.
create(FeatureOutputNames, FeatureTableCalculator<T>, LabelHeaders, FeatureExporterContext) - Static method in class FeatureExporter: Alternative static constructor that creates a shared-state from a NamedFeatureStore.
create(InputManagerParameters) - Method in class Combine
create(InputManagerParameters) - Method in class Rooted
create() - Method in class InterpolatorBeanOpenCV
create(InputManagerParameters) - Method in class ExperimentResultsExperimentStructure
create() - Static method in class ConstantsInListFixture: creates a feature-list associated with the fixture
createAddCriteria() - Method in class EnergySchemeWithSharedFeatures
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceRatioFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class SubtractReducedFromMerged
createAndConsumeListBeans(String, HierarchicalConfiguration, Object, Collection<T>) - Static method in class BeanListCreator: Extracts a list of instantiated bean objects from an XML configuration, and adds them to addTo.
createAndStartSession() - Method in class ReportFeatureEvaluator
createArguments(CommandLine) - Method in class LauncherConfig
createAscending() - Static method in class HistogramFixture: a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count 5, value 100 has count 100 etc.)
createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class AssignOverlappingObjects: Creates an assignment from the objects in left to those in right.
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class AnnotationComparisonAssigner
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class FeatureCostAssigner
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class MaskIntersectionAssigner
createAxisArray() - Method in class GradientBaseAddSum
createAxisArray() - Method in class GradientForAxis
createAxisArray() - Method in class GradientXY
createBackground(NamedProviderStore<Stack>, String) - Static method in class BackgroundCreator
createBean(Class, BeanDeclaration, Object) - Method in class DefineFactory
createBean(Class<?>, BeanDeclaration, Object) - Method in class AnchorDefaultBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class IncludeBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class IncludeListBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class ListBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class DoubleListFactory
createBean(Class, BeanDeclaration, Object) - Method in class DoubleSetFactory
createBean(Class, BeanDeclaration, Object) - Method in class IntegerListFactory
createBean(Class, BeanDeclaration, Object) - Method in class IntegerSetFactory
createBean(Class, BeanDeclaration, Object) - Method in class StringListFactory
createBean(Class, BeanDeclaration, Object) - Method in class StringSetFactory
createBean(Class, BeanDeclaration, Object) - Method in class ReplacePropertyBeanFactory
createBeanFromConfig(HierarchicalConfiguration, Object) - Static method in class BeanCreator: Creates a bean from a HierarchicalConfiguration.
createBeanFromXML(XMLBeanDeclaration, String, Object) - Static method in class BeanCreator: Creates a bean from XML.
createBetweenTwoPoints(Point3d, Point3d) - Static method in class DirectionVector: Creates a DirectionVector representing the direction between two points of type Point3d.
createBetweenTwoPoints(Point3i, Point3i) - Static method in class DirectionVector: Creates a DirectionVector representing the direction between two points of type Point3i.
createBounded(BoundingBox) - Method in interface VoxelsFactoryTypeBound: Creates and initializes voxels that correspond to a particular bounding-box region.
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in interface ArrangeStack
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Overlay
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Single
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Tile
createBufferedImage(int, int) - Method in class PlotInstance
createBuilderWithDefaultErrorHandler() - Static method in class XMLParser: Creates a document-builder with default error-handling.
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class DerivedObject
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class Erode
createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class Shell
createCalculationContext(Optional<String>, ExecutionTimeRecorder, InputOutputContext) - Method in class FeatureExporter: Creates a FeatureCalculationContext for calculating features to later use this exporter.
createCalculationContext(ExecutionTimeRecorder, InputOutputContext) - Method in class SharedStateSegmentInstance: Creates a FeatureCalculationContext for calculating features to later use this exporter.
createCalculator(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class MergedPairsFeatures
createChannel(int, boolean) - Method in class DisplayStack: Create Channel for a particular index after applying conversion.
createChannel() - Method in class CheckMarkWithMask
createChannelsForSeries(int, Progress, Logger) - Method in class NamedChannelsInput
createChart(DefaultCategoryDataset, String, Optional<AxisLimits>) - Method in class BarPlot: Creates a chart
createChart(DefaultBoxAndWhiskerCategoryDataset, String, Optional<AxisLimits>) - Method in class BoxPlot
createChart(XYDataset, String, Optional<AxisLimits>) - Method in class LinePlot: Creates a chart
createChart(S, String, Optional<AxisLimits>) - Method in class PlotIndexBase
createChecked(boolean, CheckedSupplier<T, E>) - Static method in class OptionalFactory: Like OptionalFactory.create(boolean, T) but accepts a supplier that throws a checked/exception.
createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class LevelResultCollectionFactory
createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
createColors(int) - Method in class AssignmentColorPool: Creates a list of colors to describe the assignment.
CreateCombinedStack - Class in org.anchoranalysis.image.bean.nonbean.init
createComparisonStacks(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, Logger, boolean) - Method in class MultipleComparer: Creates a Stack illustrating the comparison between annotation and each source in sources.
createContextForWriting(Optional<ImageFileFormat>, ExecutionTimeRecorder) - Method in class OutputManager: Creates the OutputWriteContext needed for writing files.
createConverter() - Method in class ConvertChannelTo
createConverter() - Method in class ConvertChannelToWithHistogram
createConverter() - Method in class ScaleByDictionary
createConverter() - Method in class ScaleByMinMaxValue
createConverter() - Method in class ScaleByTypeToByte
createConverter() - Method in class ToByte
createConverter() - Method in class ToByteUpperLowerQuantileIntensity
createCountKernelMask(ObjectMask) - Method in class TouchingVoxels
createDataset(Iterator<T>) - Method in class LinePlot
createDataset(Iterator<T>) - Method in class PlotIndexBase
createDataset(Iterator<T>) - Method in class PlotIndexBaseCategorical: Creates a sample dataset
createDefaultDataset() - Method in class BarPlot
createDefaultDataset() - Method in class BoxPlot
createDefaultDataset() - Method in class PlotIndexBaseCategorical
createDelegate(Feature<T>) - Method in class PermuteDivideByParam
createDelegate(Feature<T>) - Method in class PermuteFeatureSequenceInteger
createDelegate(Feature<T>) - Method in class PermuteFirstSecondOrder
createDescending() - Static method in class HistogramFixture
createDescriptor(Extent) - Method in class HOGParameters: Creates an empty HOGDescriptor to describe an image of a particular size.
createDesignMatrix(List<Point3f>) - Method in class LinearLeastSquaresViaNormalEquationBase
createDictionary() - Method in class EnergyScheme: returns the associated Dictionary or an empty set, if no dictionary is associated with the energy-scheme.
createDim() - Method in class PointsFitterToMark
createDimensions() - Method in class WithDimensionsBase
createDims() - Method in class WithOptionalDimensionsBase: Returns the dimensions or null if none are provided
createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, float) - Method in class DistanceTransform3D
createDuplicatePxlMarkMemoList() - Method in class VoxelizedMarksWithEnergy
CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
CreateEllipse() - Constructor for class CreateEllipse
createEmpty(Extent, VoxelDataType) - Method in class VoxelsFactory: Creates empty voxels to match a particular size.
createEmptyInitialised(Dimensions) - Method in class ChannelFactorySingleType: Create a Channel initialized with zero-valued voxel-buffers.
createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class ChannelFactory: Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value.
createEmptyMat(Extent, int) - Static method in class ConvertToMat: Creates a Mat which contains only zero-values.
createEmptyOff(Extent) - Static method in class BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
createEmptyOff(Extent, VoxelDataType) - Static method in class BinaryVoxelsFactory: Creates an empty binary-voxels of a particular data-type with all voxels initialized to off.
createEmptyOn(Extent) - Static method in class BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on (255).
createEmptyStackFor(Dimensions) - Static method in class ObjectsAsRGBGenerator
createEmptyUninitialised(Dimensions) - Method in class ChannelFactorySingleType: Create a Channel without initialization with voxel-buffers.
CreateException - Exception in org.anchoranalysis.core.exception: A generic exception that be thrown when the creation of a new object fails.
CreateException(String) - Constructor for exception CreateException: Creates with a message, but without a cause.
CreateException(Throwable) - Constructor for exception CreateException: Creates with a cause, but without a message.
CreateException(String, HasFriendlyErrorMessage) - Constructor for exception CreateException: Creates with a message, and a cause with a user-friendly error message.
CreateException(String, AnchorCombinableException) - Constructor for exception CreateException: Creates with a message, and a combinable-exception as a cause.
createExperimentExecutor(CommandLine) - Method in class LauncherConfig
createExperimentOutputter(Optional<String>, Manifest, MultiLevelOutputEnabled, Optional<MultiLevelRecordedOutputs>, OutputWriteContext, PathPrefixerContext, Optional<Logger>) - Method in class OutputManager: Creates an outputter for the experiment in general.
createExperimentState() - Method in class SegmentIntoMarks
createExperimentState() - Method in class SegmentWithMarkedPointProcess
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider>>, FeatureOutputNames, FeatureExporterContext) - Method in class FeatureSource: Creates the FeatureExporter to be used for calculating and exporting feature-results.
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, FeatureOutputNames, FeatureExporterContext) - Method in class SingleRowPerInput
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, FeatureOutputNames, FeatureExporterContext) - Method in class FromObjects
CreateFeatureInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session
createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueIndividualEnergyGreaterThan
createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueMarkGreaterEqualThan
createFeatureList(String, TestLoader) - Static method in class FeaturesFromXmlFixture
createFeatureNames() - Method in interface FeatureTableCalculator: Creates A list of names for each feature (columns of the table)
createFeatureNames() - Method in class PairsTableCalculator
createFeatureNames() - Method in class SingleTableCalculator
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class CombineObjectsForFeatures: Creates features that will be applied on the objects.
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class EachObjectIndependently
createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class EachObjectIndependently
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class PairNeighbors
createFeatureSession() - Method in class FeatureEvaluator: Creates session for evaluating feature optionally adding an energy-stack.
createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class FeatureListEvaluator: Creates session for evaluating features.
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class AlwaysAllowed
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class CheckIfAllowed
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in interface Writer: The path to write a particular output to.
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class WriterRouterErrors: The path to write a particular output to.
createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>, String) - Static method in class CSVReporterUtilities
createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class EllipsoidFitHelper
createFlat(boolean, Supplier<Optional<T>>) - Static method in class OptionalFactory: Creates an Optional from a boolean flag and a supplier that returns an Optional.
createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class VoxelsArithmeticFactory: Create a VoxelsArithmetic for FloatBuffer.
createFloat(Voxels<FloatBuffer>, int) - Static method in class VoxelsAssignerFactory: Create a VoxelsAssigner for a FloatBuffer.
createFloat(Extent) - Static method in class MaxIntensityProjection: Creates a buffer for a max-intensity projection for float voxels.
createFloat(Extent) - Static method in class MeanIntensityProjection: Creates a buffer for a mean-intensity projection for float voxels.
createFloat(Voxels<FloatBuffer>) - Static method in class VoxelsExtracterFactory: Create voxels-extracter for FloatBuffer.
createForDirectoryPermissive(Path, boolean, Optional<Logger>) - Static method in class OutputterChecked: Creates, defaulting to a permissive output-manager in a particular directory.
createForFeature(Feature<?>) - Method in interface CreateFeatureInput
createForSingle(AnchorBean<?>, String) - Static method in class PermutationAssignerFactory: Creates an assigner for one or more properties, as identified by propertyPath.
createForSubdirectory(String) - Method in class TestLoader: Creates a new test-loader for a subdirectory of the current test.
createForVoxelBuffer(VoxelBuffer<T>, Extent) - Method in interface VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with a single-slice's memory buffers.
createFrom(BufferedImage) - Static method in class CreateStackFromBufferedImage: Create a Stack by converting a BufferedImage.
createFrom(Mask, int, boolean, boolean) - Static method in class FindContour: Creates an contour from a Mask at the boundary of depth 1 pixel.
createFrom(ObjectMask, int, boolean, boolean) - Static method in class FindContour: Creates an contour from a ObjectMask.
createFrom(VoxelsUntyped, Optional<ObjectMask>) - Static method in class HistogramFromObjectsFactory: Creates a Histogram of voxel intensity values in voxels, all or only those in object.
createFrom(Channel, ObjectMask) - Static method in class HistogramFromObjectsFactory: Creates a Histogram of voxel intensity values in channel corresponding to object.
createFrom(Channel, ObjectCollection) - Static method in class HistogramFromObjectsFactory: Creates a Histogram of voxel intensity values in channel corresponding to objects.
createFrom(Channel, Mask) - Static method in class HistogramFromObjectsFactory: Creates a Histogram of all voxel intensity values in channel corresponding to Mask.
createFrom(int, ObjectMask) - Method in interface DecodeLabels.CreateElementFromScaledObject: Create from an index and it's scaled-object.
createFrom(int, ObjectMask) - Method in interface AccessObjectMask: Creates an element of type T from an object-representation and index.
createFrom(int, ObjectMask) - Method in class AccessObjectMaskSimple
createFrom(SliceBufferIndex<T>, VoxelDataType) - Method in class VoxelsFactory: Creates voxels from a particular SliceBufferIndex with specified type.
createFrom(VoxelBuffer<?>) - Static method in class HistogramFactory: Creates a Histogram of the aggregated voxel intensities in a VoxelBuffer.
createFrom(VoxelsUntyped) - Static method in class HistogramFactory: Creates a Histogram of the aggregated voxel intensities in a VoxelsUntyped.
createFromChannel(Channel) - Method in class ChannelProviderUnary
createFromChannel(Channel) - Method in class AnisotropicDiffusion
createFromChannel(Channel) - Method in class MinimumFilter
createFromChannel(Channel) - Method in class Invert
createFromChannel(Channel) - Method in class AssignFromDictionary
createFromChannel(Channel) - Method in class AssignFromIntersectingObjects
createFromChannel(Channel) - Method in class Convert
createFromChannel(Channel) - Method in class ConvertWithHistogram
createFromChannel(Channel) - Method in class Duplicate
createFromChannel(Channel) - Method in class GradientBaseAddSum
createFromChannel(Channel) - Method in class Sobel
createFromChannel(Channel) - Method in class IfParamEquals
createFromChannel(Channel) - Method in class Blur
createFromChannel(Channel) - Method in class IfVoxelZero
createFromChannel(Channel) - Method in class Median
createFromChannel(Channel, ObjectCollection) - Method in class NormalizeDifferenceToMedian
createFromChannel(Channel, ObjectCollection) - Method in class NormalizeObjectIntensity
createFromChannel(Channel) - Method in class QuantileStretch
createFromChannel(Channel) - Method in class ScaleXY
createFromChannel(Channel) - Method in class UnaryWithMaskBase
createFromChannel(Channel) - Method in class LevelPerObjectBase
createFromChannel(Channel, ObjectCollection) - Method in class IdentifyObjects
createFromChannel(Channel, ObjectCollection) - Method in class ScoreObjects
createFromChannel(Channel) - Method in class ExtractCenterSlice
createFromChannel(Channel) - Method in class ExtractSliceRange
createFromChannel(Channel) - Method in class MaximumIntensityProjection
createFromChannel(Channel) - Method in class MeanIntensityProjection
createFromChannel(Channel) - Method in class UnaryWithObjectsBase
createFromChannel(Channel, ObjectCollection) - Method in class UnaryWithObjectsBase
createFromChannel(Channel) - Method in class UnaryWithValueBase
createFromChannel(Channel) - Method in class SegmentChannel
createFromChannel(Channel) - Method in class SegmentWithSeeds
createFromChannel(Channel) - Method in class WithChannelBase
createFromChannel(Channel, int) - Method in class BackgroundSubtractor
createFromChannel(Channel) - Method in class EdgeFilterIJ
createFromChannel(Channel) - Method in class GaussianBlur2D
createFromChannel(Channel) - Method in class MedianFilter3D
createFromChannel(Channel, int) - Method in class WithFilterBase
createFromChannel(Channel) - Method in class WithRadiusBase
createFromChannel(Channel, int) - Method in class WithRadiusBase
createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantBase
createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantConditionallyWriteBase
createFromChannelWithConstant(Channel, double) - Method in class UnaryWithValueBase
createFromDimensions(Dimensions) - Method in class DistanceTransformForEachObject3D
createFromDimensions(Dimensions) - Method in class CreateNew
createFromDimensions(Dimensions) - Method in class FromDimensionsBase
createFromDimensions(Dimensions) - Method in class RepeatSlice
createFromDimensions(Dimensions) - Method in class AllValuesOff
createFromDimensions(Dimensions) - Method in class AllValuesOn
createFromDimensions(Dimensions) - Method in class FromObjects
createFromDimensions(Dimensions) - Method in class FromDimensionsBase
createFromDimensions(Dimensions) - Method in class Box
createFromExisting(InitializationContext, Optional<Define>, Optional<SharedObjects>, Optional<Dictionary>) - Static method in class MarksInitializationFactory
createFromExplicitDirectory(String) - Static method in class TestLoader: Creates a new test-data loader using an explicit file path as root.
createFromExplicitDirectory(Path) - Static method in class TestLoader: Creates a new test-data loader using an explicit file path as root.
createFromFile(Path) - Method in class DeriveElementsFromSequencedDirectory: Creates an element of type T from a one particular file in the sequence.
createFromFile(Path) - Method in class SequencedDirectoryDeserializer
createFromGenerator(TransformingGenerator<BoundingBox, Stack>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator: Creates an extracted-object generator that draws an outline - with default color green and flattened in Z.
createFromGuess3D(Mask, int, boolean, boolean) - Static method in class FindContour: Like FindContour.createFrom(Mask, int, boolean, boolean), but guesses whether to do this in 2D or 3D.
createFromHistogram(Histogram) - Method in class HistogramProviderUnary
createFromHistogram(Histogram) - Method in class CutBelowThreshold
createFromHistogram(Histogram) - Method in class GreaterThanThreshold
createFromList(List<T>, Function<T, BoundingBox>) - Static method in class BoundedList: Creates for a list, minimally fitting a bounding-box around all elements
createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class VoxelizedMarksWithEnergyFactory
createFromMask(Mask) - Method in class MaskProviderUnary
createFromMask(Mask) - Method in class DistanceTransform3D
createFromMask(Mask) - Method in class FromMask
createFromMask(Mask) - Method in class FromMaskBase
createFromMask(Mask) - Method in class CombineBase
createFromMask(Mask) - Method in class Duplicate
createFromMask(Mask) - Method in class Invert
createFromMask(Mask) - Method in class ExteriorContour
createFromMask(Mask) - Method in class FitBoxToOnVoxels
createFromMask(Mask) - Method in class MorphologicalOperatorBase
createFromMask(Mask) - Method in class IfPredicateBase
createFromMask(Mask) - Method in class ScaleXY
createFromMask(Mask) - Method in class FlattenZ
createFromMask(Mask) - Method in class RepeatSlice
createFromMask(Mask) - Method in class FillHoles
createFromMask(Mask) - Method in class MorphologicalOperation
createFromMask(Mask, Mask) - Method in class ConvexHull2D
createFromMask(Mask, Mask) - Method in class ConvexHull3D
createFromMask(Mask) - Method in class ConvexHullBase
createFromMask(Mask, Mask) - Method in class ConvexHullBase
createFromMaskedChannel(Channel, Mask) - Method in class SubtractMean
createFromMaskedChannel(Channel, Mask) - Method in class AssignFromChannel
createFromMaskedChannel(Channel, Mask) - Method in class AssignValue
createFromMaskedChannel(Channel, Mask) - Method in class UnaryWithMaskBase
createFromMaskedChannel(Channel, Mask) - Method in class ZeroOutsideMask
createFromMavenWorkingDirectory() - Static method in class TestLoader: Creates a new test-data loader finding PATH_RESOURCES using the Maven working directory.
createFromMavenWorkingDirectory(String) - Static method in class TestLoader: Creates a new test-data loader finding PATH_RESOURCES/PLUS_SOMETHING using the Maven working directory.
createFromNotObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class MaskFromObjects: Create a Mask corresponding to all off voxels in an ObjectCollection.
createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderUnary
createFromObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class MaskFromObjects: Create a Mask corresponding to all on voxels in an ObjectCollection.
createFromObjects(ObjectCollection) - Method in class AtIndex
createFromObjects(ObjectCollection) - Method in class DecomposeIntoConnectedComponents
createFromObjects(ObjectCollection) - Method in class RejectIfNotConnected
createFromObjects(ObjectCollection) - Method in class Duplicate
createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeature
createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
createFromObjects(ObjectCollection) - Method in class SortByFeature
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class Filter
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class FilterByGroup
createFromObjects(ObjectCollection) - Method in class IntersectsWithContainer
createFromObjects(ObjectCollection) - Method in class Match
createFromObjects(ObjectCollection) - Method in class NotInContainer
createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderFilterBase
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class ObjectCollectionProviderFilterBase
createFromObjects(ObjectCollection) - Method in class RemoveTouchingBorder
createFromObjects(ObjectCollection) - Method in class AndObjectsWithMasks
createFromObjects(ObjectCollection) - Method in class MergeGreedyToIncreaseObjectFeature
createFromObjects(ObjectCollection) - Method in class MergeWithFeature
createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderMorphological
createFromObjects(ObjectCollection) - Method in class Scale
createFromObjects(ObjectCollection, Channel) - Method in class BinarySegmentByObject
createFromObjects(ObjectCollection, Channel) - Method in class SegmentChannelByObject
createFromObjects(ObjectCollection) - Method in class ExtendInZ
createFromObjects(ObjectCollection) - Method in class ExtendInZWithinContainer
createFromObjects(ObjectCollection) - Method in class FlattenZ
createFromObjects(ObjectCollection) - Method in class SliceAt
createFromObjects(ObjectCollection) - Method in class RemoveIntersectingVoxels
createFromObjects(ObjectCollection) - Method in class SplitByObjects
createFromObjects(ObjectCollection) - Method in class SplitIntoSquares
createFromObjects(ObjectCollection) - Method in class UnaryWithChannelBase
createFromObjects(ObjectCollection, Channel) - Method in class UnaryWithChannelBase
createFromObjects(ObjectCollection) - Method in class DrawLineAlongConvexHull
createFromObjects(ObjectCollection) - Method in class FillHoles
createFromObjects(ObjectCollection) - Method in class MergeSpatialClusters
createFromObjects(ObjectCollection) - Method in class SplitContourAtSaddlePoints
createFromOutputter(String, OutputterChecked) - Static method in class CSVWriter: Creates and starts a CSVWriter if it's allowed, otherwise returns Optional.empty().
createFromOutputterWithHeaders(String, OutputterChecked, Supplier<List<String>>, ErrorReporter) - Static method in class CSVWriter: Like CSVWriter.createFromOutputter(String, OutputterChecked) but suppresses any exceptions into an error log - and writes headers.
createFromOverlays(ColoredOverlayCollection, IdentifierGetter<Overlay>, IdentifierGetter<ObjectWithProperties>) - Static method in class ObjectDrawAttributesFactory
createFromPath(Path, Logger) - Static method in class ObjectCollectionReader: Reads an object-collection from a path (or path prefix) trying different methods to read the objects.
createFromPathCached(CheckedSupplier<Path, OperationFailedException>, Logger) - Static method in class ObjectCollectionReader
createFromSource(Channel) - Method in class AutoLocalThreshold
createFromSource(Channel) - Method in class FromChannel
createFromSource(Channel) - Method in class FromChannelBase
createFromSource(Channel) - Method in class SegmentChannel
createFromSource(Channel) - Method in class Threshold
createFromStack(Stack) - Method in class StackProviderUnary
createFromStack(ScaleableBackground, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator: Creates the generator with a stack as the background - and with default color green and flattened across the Z-dimension.
createFromStack(Optional<ScaleableBackground>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator: Creates the generator with maybe a stack as the background, or else an empty background - and with default color green and flattened in Z
createFromStack(Stack) - Method in class MontageSlices
createFromStack(Stack) - Method in class ColorConverterBase
createFromString(String) - Static method in class AxisConverter: Maps a string of x, y, z (case ignored) to a corresponding axis type.
createFromTupleDuplicate(ReadableTuple3i) - Static method in class Extent: Creates from a ReadableTuple3i representing the sizes in each dimension, where the tuple is not used internally.
createFromTupleReuse(ReadableTuple3i) - Static method in class Extent: Creates from a ReadableTuple3i representing the sizes in each dimension, where the tuple is used internally.
createFromTwoMasks(Mask, Mask) - Method in class And
createFromTwoMasks(Mask, Mask) - Method in class CombineBase: Creates masks from some combination of two masks
createFromTwoMasks(Mask, Mask) - Method in class IfHighLow
createFromTwoMasks(Mask, Mask) - Method in class Or
createFromTwoMasks(Mask, Mask) - Method in class Xor
createGenerator() - Method in class CombineRasterGenerator
createGenerator() - Method in class TextStyle: Creates a generator, which produces a drawn string on an image when generated
createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class BufferedImageFromVoxels: Creates a BufferedImage from a Voxels<UnsignedByteBuffer>.
createGrayscaleShort(Voxels<UnsignedShortBuffer>) - Static method in class BufferedImageFromVoxels: Creates a BufferedImage from a Voxels<UnsignedShortBuffer>.
createGroupMap(ConsistentChannelChecker) - Method in class GroupedStackBase: Creates a map for the storing an aggregate-data-object for each group.
createGroupMap(ConsistentChannelChecker) - Method in class ExportImageHistograms
createGroupMap(ConsistentChannelChecker) - Method in class GroupedMeanChannelTask
createHashMapToId() - Method in class MarkCollection
createHeaders(String[], Optional<String>, boolean) - Static method in class LabelHeadersForCSV: Creates the label-headers (the headers for columns not associated with features).
createIdArr() - Method in class MarkCollection
createIdHashMap() - Method in class MarkCollection
createImageDim() - Method in class ReportFeatureForMarks
createImageFormat(String) - Static method in class FileFormatFactory: Creates a ImageFileFormat from an identifier string if its equal to any extension associated with the image file formats in ImageFileFormat.
createInitialization(InitializationContext, ExportSharedObjects) - Method in class DefineOutputter
createInitialization(InitializationContext, Optional<SharedObjects>, Optional<Dictionary>) - Method in class DefineOutputter
createInitializationContext() - Method in class InputBound
createInitializationContext() - Method in class ParametersExperiment
createInitialized(Extent) - Static method in class FromByte: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class FromFloat: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class FromInt: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class FromShort: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Method in interface VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with memory buffers.
createInputContext() - Method in class ExecutionArguments: Creates an input-context, reusing parameters from the experiment-execution
createInputsFromFiles(FilesProvider, InputManagerParameters, Function<NamedFile, T>) - Method in class NamedFilesBase: Creates a list of inputs from a FilesProvider which together with the namer can create the inputs.
createIntersectionComplement(ColoredOverlayCollection, ColoredOverlayCollection) - Static method in class ColoredOverlayCollection
createInverted() - Method in class BinaryValuesInt: Inverts the values so off becomes on, and vice-versa.
createKernel() - Method in class DilationContext: Creates a kernel for performing the dilation.
createKernelFactoryNames() - Method in class KernelProposer
createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class LabelObjects: Creates a channel that contains a unique integer (label) for each element's object-representation.
createList(int) - Method in class ColorScheme: Creates a sequence of related colors.
createList(int) - Method in class ColorSchemeUnary
createList(int) - Method in class FromList
createList(int) - Method in class FromSingle
createList(int) - Method in class HSB
createList(int) - Method in class VeryBright
createListBeans(String, HierarchicalConfiguration, Object) - Static method in class BeanListCreator: A list of instantiated bean objects from an XML configuration.
createListChildFeatures() - Method in class Feature: Returns a list of Features that exist as bean-properties of this feature, either directly or in lists.
createListMembershipWithFlags() - Method in class RegionMap
createManifestDescription() - Method in class AssignmentGenerator
createManifestDescription() - Method in class ChannelGenerator
createManifestDescription() - Method in class ObjectsAsGrayscaleGenerator
createManifestDescription() - Method in class HDF5ObjectsGenerator
createManifestDescription() - Method in class ObjectAsMaskGenerator
createManifestDescription() - Method in class ObjectsAsRGBGenerator
createManifestDescription() - Method in class DrawObjectOnStackGenerator
createManifestDescription() - Method in class ExtractBoundingBoxAreaFromStackGenerator
createManifestDescription() - Method in class RasterGenerator
createManifestDescription() - Method in class RasterGeneratorDelegateToDisplayStack
createManifestDescription() - Method in class RasterGeneratorDelegateToRaster
createManifestDescription() - Method in class RGBTimeSeriesGenerator
createManifestDescription() - Method in class StackGenerator
createManifestDescription(String) - Static method in class CollectionGenerator
createManifestDescription() - Method in class DictionaryGenerator
createManifestDescription() - Method in class SerializedGenerator
createManifestDescription() - Method in class SingleFileTypeGenerator
createManifestDescription() - Method in class SingleFileTypeGeneratorBridge
createManifestDescription() - Method in class CSVGenerator
createManifestDescription() - Method in class StringGenerator
createManifestDescription() - Method in class MarksAsUniqueValueGenerator
createManifestDescription() - Method in class MarksGeneratorBase
createMap(OpenedImageFile, Logger) - Method in class ChannelMap
createMap(OpenedImageFile, Logger) - Method in class Autoname
createMap(OpenedImageFile, Logger) - Method in class FromEntries
createMap(OpenedImageFile, Logger) - Method in class FromMetadata
createMap(OpenedImageFile, Logger) - Method in class SingleChannel
createMapToIndex() - Method in class FeatureNameList: Creates a map from the feature-names to their indices in the list.
createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class EllipsoidFactory: Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an object-mask
createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class EllipsoidFactory
createMarkFromPoint(Point3i, int, boolean) - Static method in class MarkConicFactory
createMarkFromPoint(Point3d, int, boolean) - Static method in class MarkConicFactory
CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
CreateMarkFromPoints() - Constructor for class CreateMarkFromPoints
createMarkFromPoints3f(List<Point3f>) - Static method in class PointListFactory
createMarkFromPoints3i(List<Point3i>) - Static method in class PointListFactory
createMaskOff(Dimensions) - Static method in class MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to off.
createMaskOff(Dimensions, BinaryValuesInt) - Static method in class MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to off.
createMaskOn(Dimensions) - Static method in class MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to on.
createMaskOn(Dimensions, BinaryValuesInt) - Static method in class MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to on.
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchExtensions
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchGlob
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchRegularExpression
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class PathMatcher
createMerged(ColoredMarks) - Method in class ColoredMarks
createMerged(MarkCollection) - Method in class MarkCollection
createMerged(OverlayCollection) - Method in class OverlayCollection
createMessageForDescription(String) - Method in exception BeanMisconfiguredXMLException
createMessageForDescription(String) - Method in exception LocalisedBeanException
createMessageForDescription(String) - Method in exception AnchorCombinableException: Creates a message for the exception from the description.
createMessageForDescription(String) - Method in exception NamedProviderGetException
createMinusOne() - Method in class Extent: Creates a new Extent with each dimension decreased by one.
createMockFeatureWithCalculation() - Static method in class MockFeatureWithCalculationFixture: Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the number of pixels in an object
createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class MockFeatureWithCalculationFixture: Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result calculated using a lambda
createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentObjectsFromONNXModel
createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentObjectsFromTensorFlowModel
createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class NamedFeatureStoreFactory: Create a NamedFeatureStore from a list of beans.
createNamedFeatureProviders(String, TestLoader) - Static method in class FeaturesFromXmlFixture
createNecessaryDirectories(Path) - Static method in class DirectoryCreator: Creates necessary directories to make a path to a file valid.
CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Creates a new channel with all values initialized to a constant (by default zero)
CreateNew() - Constructor for class CreateNew
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
CreateNew() - Constructor for class CreateNew
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a new empty collection of marks
CreateNew() - Constructor for class CreateNew
createNewDocument() - Static method in class XMLParser: Creates a new XML document.
createNext(int, int) - Method in interface TableItemArrangement.TableCreator
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class OverlayMark
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class Overlay
createObjects() - Method in class PointsFitterToMark
createObjectsImage(Assignment<ObjectMask>, boolean, AssignmentColorPool) - Method in class DrawColoredObjects: Creates an image with the objects colored, as indicated in the class description.
createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class GeneratorBridge: Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class GeneratorBridge: Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
createOrderProvider() - Method in class IncreasingIntegers
createOrderProvider() - Method in class IncrementingIntegers
createOrderProvider() - Method in class SequenceType
createOrderProvider() - Method in class StringsWithoutOrder
createOrReuse(Throwable) - Static method in exception InitializeException: Wraps exception in a InitializeException, unless it already its cause is a InitializeException.
createOrReuse(T) - Method in class AlwaysNew
createOrReuse(T) - Method in class CacheAndReuseStrategy
createOrReuse(T) - Method in interface ReplaceStrategy
createOrReuse(T) - Method in class ReuseSingletonStrategy
createOutPathString() - Method in class AppendCsv
createOutPathString() - Method in class AppendDictionary
createOutPathString() - Method in class AppendFilePath
createOutPathString() - Method in class AppendHistogram
createOutPathString() - Method in class AppendMarks
createOutPathString() - Method in class AppendObjects
createOutPathString() - Method in class AppendStack
createOutPathString() - Method in class AppendStackDirect
createOutPathString() - Method in class FilePathAppendBase
createPair(CreateCalculatorHelper, ImageInitialization, CacheTransferSourceCollection) - Method in class MergedPairsFeatures
createPairsUnique() - Method in class RandomCollectionWithAddCriteria
createPairsUnique() - Method in class EnergySavedPairs
createParam(String, boolean) - Method in class PermuteFeatureSequenceInteger
createParameters() - Method in class TouchingVoxels
createParameters(boolean, boolean) - Method in class SurfaceNumberVoxelFaces
createParameters(boolean, boolean) - Method in class SurfaceNumberVoxels
createParameters(boolean, boolean) - Method in class SurfaceNumberVoxelsBase
createPathDeriver(String, String) - Method in class FilePathAppendBase: Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups The first group should correspond to top-level folder for the project The second group should correspond to the unique name of the dataset.
createPayloadCalculator() - Method in class MergePairs
createPayloadCalculator() - Method in class MergeToIncreaseObjectFeature
createPayloadCalculator() - Method in class MergeWithFeature: Determines the payload for any given or potential vertex
createPermutedCopies(List<T>, PermuteProperty<S>, PermutationAssigner) - Method in class PermutedCopyCreator: Applies a permutation to a copy of each element in a list of beans, updating the custom name of each bean to reflect the permutation.
createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeature
createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureBase
createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureSequenceInteger
createPolicy() - Method in class ConvertBase
createPrecalc(DrawOverlay, ObjectWithProperties, Dimensions) - Static method in class DrawOverlay
createPrefixerContext() - Method in class ExecutionArguments
createPrioritizer() - Method in class MergePairs
createPrioritizer() - Method in class MergeToIncreaseObjectFeature
createPrioritizer() - Method in class MergeWithFeature: Determines the priority (and selection criteria) used to allow merges between neighbors
createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface Prioritizer
createRadiiArray() - Method in class ConicBase
createRadiiArray() - Method in class Ellipse
createRadiiArray() - Method in class Ellipsoid
createRadiiArrayResolved(Optional<Resolution>) - Method in class ConicBase
createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipse
createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipsoid
createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class BufferedImageFromStack: Creates a BufferedImage from three Voxels<UnsignedByteBuffer> representing respectively, red, green, blue color components.
createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class ThreeChannels
createRoot() - Static method in class ProposerFailureDescription
createRow(String[]) - Method in class ColumnDefinition
createSameSize(ChannelProvider, String, Channel) - Static method in class DimensionsChecker: Creates a new channel from a provider, making sure it's the same size as an an existing channel
createSameSize(MaskProvider, String, Channel) - Static method in class DimensionsChecker: Creates a new channel from a provider, making sure it's the same size as an an existing channel
createScaledObject(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in class FromMask
createScaledObject(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in interface ScaledOverlayCreator: Creates a scaled-version of the object to use as an overlay..
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class OverlayMark
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class Overlay
createSecondLevelFromSet(StringSet) - Method in class AddToDefaults
createSecondLevelFromSet(StringSet) - Method in class IgnoreUnderscorePrefixUnless
createSecondLevelFromSet(StringSet) - Method in class NoneExcept
createSecondLevelFromSet(StringSet) - Method in class OutputEnableRulesSpecify: Creates a new second-level SingleLevelOutputEnabled from the relevant set of strings.
createSecondLevelFromSet(StringSet) - Method in class PermissiveExcept
createSequence(VoxelDataType) - Method in class MultiBufferSized
createSession() - Method in class ObjectCollectionProviderWithFeature
createSet() - Method in class MarkCollection
createSet() - Method in class ColoredOverlayCollection
createSet() - Method in class OverlayCollection
createSetter(AnchorBean<?>) - Method in class PermuteProperty: Creates a PermutationAssigner which allows the particular property to be changed.
createSharedStateJob(InputOutputContext) - Method in class ConvertImageFormat: Sets a new output-sequence for the series.
createSharedStateJob(InputOutputContext) - Method in class RasterTask: Creates a shared-state for the duration of a particular input-job
createSharedStateJob(InputOutputContext) - Method in class MovieFromSlices
createSingle(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class MergedPairsFeatures
createSingle(T, Function<T, BoundingBox>) - Static method in class BoundedList: Creates for a single element using its current bounding-box.
createSingleStack() - Method in class StackSeries: Puts all stacks in the series into a single image stack
createStack(List<RGBStack>, ChannelFactorySingleType) - Method in class RasterArranger
CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.bufferedimage: Converts a BufferedImage from the AWT library to a Stack.
createStackProvider(List<StackProviderWithLabel>, int, boolean, boolean, boolean) - Static method in class TileRasters
createStackSequenceForSeries(int, Logger) - Method in interface StackSequenceInput: Creates a supplier of a TimeSequence of stacks for a particular series number.
createStackSequenceForSeries(int, Logger) - Method in class ConvertNamedChannelsInputToStack
createStatistics() - Method in class ConcurrentJobMonitor
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class MarkRegion
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class CenterSliceBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class GreatestAreaSlice
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class IndexedRegionBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class IndexedRegionBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class MaxNonZero
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class SelectSlicesWithIndexBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class Specific
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class Thresholded
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSlice
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceBase
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceWindow
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class AlwaysAllowed
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class CheckIfAllowed
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in interface Writer: Maybe creates a subdirectory for writing to.
createSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class WriterRouterErrors: Maybe creates a subdirectory for writing to.
createSubset(Collection<Integer>) - Method in class ObjectCollection: A subset of the collection identified by particular indices.
createSubset(IntPredicate) - Method in class OverlayCollection
createSubsetFromIDs(IntPredicate) - Method in class ColoredOverlayCollection
createToColorUnselectedObjects() - Static method in class OutlinePreserveRelativeSize: Alternative constructor that switches on the coloring of unselected objects by default.
createTransformerFactory() - Static method in class XMLParser: Creates a TransformerFactory that ignores any DTDs in the document and disables external entities (to prevent XXE attacks).
createUninitialised(Dimensions, VoxelDataType) - Method in class ChannelFactory: Create a Channel without initialization with voxel-buffers.
createUninitialized(Extent) - Static method in class FromByte: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class FromFloat: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class FromInt: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class FromShort: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Method in interface VoxelsFactoryTypeBound: Create a new Voxels that has not yet been initialized with memory buffers.
createUnsignedByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedByteBuffer.
createUnsignedByte(Voxels<UnsignedByteBuffer>, int) - Static method in class VoxelsAssignerFactory: Create a VoxelsAssigner for a UnsignedByteBuffer.
createUnsignedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class ObjectsFromConnectedComponentsFactory: Finds the connected-components in unsigned byte voxels.
createUnsignedByte(Extent) - Static method in class MaxIntensityProjection: Creates a buffer for a max-intensity projection for unsigned byte voxels.
createUnsignedByte(Extent) - Static method in class MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned byte voxels.
createUnsignedByte(Voxels<UnsignedByteBuffer>) - Static method in class VoxelsExtracterFactory: Create voxels-extracter for UnsignedByteBuffer.
createUnsignedInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedIntBuffer.
createUnsignedInt(Voxels<UnsignedIntBuffer>, int) - Static method in class VoxelsAssignerFactory: Create a a VoxelsAssigner for a UnsignedIntBuffer.
createUnsignedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class ObjectsFromConnectedComponentsFactory: Finds the connected-components in unsigned int voxels.
createUnsignedInt(Extent) - Static method in class MaxIntensityProjection: Creates a buffer for a max-intensity projection for unsigned int voxels.
createUnsignedInt(Extent) - Static method in class MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned int voxels.
createUnsignedInt(Voxels<UnsignedIntBuffer>) - Static method in class VoxelsExtracterFactory: Create voxels-extracter for UnsignedIntBuffer.
createUnsignedShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedShortBuffer.
createUnsignedShort(Voxels<UnsignedShortBuffer>, int) - Static method in class VoxelsAssignerFactory: Create a VoxelsAssigner for a UnsignedShortBuffer.
createUnsignedShort(Extent) - Static method in class MaxIntensityProjection: Creates a buffer for a max-intensity projection for unsigned short voxels.
createUnsignedShort(Extent) - Static method in class MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned short voxels.
createUnsignedShort(Voxels<UnsignedShortBuffer>) - Static method in class VoxelsExtracterFactory: Create voxels-extracter for UnsignedShortBuffer.
createVector() - Method in class AxisAlignedUnitVector
createVector() - Method in class DirectionVectorBean: Creates a vector in a particular direction
createVector() - Method in class VectorInDirection
createWithConsoleFallback(OutputterChecked, ExecutionArguments, boolean) - Method in class LoggingDestination: Creates a logger for this destination - and if anything goes wrong reporting fallback into the console.
createWithEmptyBackground(int, ColorIndex) - Static method in class DrawObjectOnStackGenerator: Creates the generator with an empty background - and with default color green and flattened in Z
createWithEmptyList() - Static method in class SpecificPathList: Factory method for creating the class with an empty list of paths
createWithLeftUnassigned(ObjectCollection) - Static method in class OverlappingObjects: Creates with only left unassigned objects.
createWithLogFallback(OutputterChecked, MessageLogger, ExecutionArguments, boolean) - Method in class LoggingDestination: Creates a logger for this destination - and if anything goes wrong reporting fallback into a log.
createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
createWithoutColor(ObjectCollection, IdentifierGetter<ObjectMask>) - Static method in class OverlayCollectionObjectFactory
createWithoutStacks(InitializationContext) - Static method in class InitializationFactory
createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteContext, Optional<WriteOperationRecorder>, Optional<MultiLevelRecordedOutputs>, boolean, Optional<Logger>) - Static method in class OutputterChecked: Creates a bound output-manager from an existing OutputManager with a prefix.
createWithRangeLimits(Iterator<T>, Optional<AxisLimits>) - Method in class PlotIndexBase
createWithRight(ObjectCollection) - Static method in class OverlappingObjects: Creates with only right unassigned objects.
createWithStacks(ProvidesStackInput, InitializationContext) - Static method in class InitializationFactory
createWithXY(double) - Static method in class Resolution: Creates with only XY resolution, identical in both dimensions.
createWithXYAndZ(double, double) - Static method in class Resolution: Creates with XY resolution and Z resolution.
createWriter() - Method in class BioformatsWriter: Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
createWriter() - Method in class OMETiff
createWriter() - Method in class OMEXML
createWriter() - Method in class Tiff
createWriter(OutputterChecked) - Method in class ExportReportFeatures
cropRemoveLargerValues(long) - Method in class Histogram: Like Histogram.cropRemoveSmallerValues(long) but larger values are removed rather than smaller values if the total count is too high.
cropRemoveSmallerValues(long) - Method in class Histogram: Creates a Histogram reusing the bins in the current histogram, but with an upper limit on the total count.
crossProduct(Vector3d) - Method in class Vector3d: Computes the cross-product of the tuple with another.
CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
CSVGenerator(String) - Constructor for class CSVGenerator
CSVReader - Class in org.anchoranalysis.io.input.csv: Reads a CSV File from the file-system.
CSVReader(String, boolean) - Constructor for class CSVReader
CSVReader(String, boolean, boolean) - Constructor for class CSVReader
CSVReader.OpenedCSVFile - Class in org.anchoranalysis.io.input.csv
CSVReaderByLine - Class in org.anchoranalysis.io.input.csv: Reads a CSV file line-by-line.
CSVReaderByLine.ProcessCSVLine - Interface in org.anchoranalysis.io.input.csv
CSVReaderException - Exception in org.anchoranalysis.io.input.csv
CSVReaderException(String) - Constructor for exception CSVReaderException
CSVReaderException(Throwable) - Constructor for exception CSVReaderException
CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Outputs statistics on current energy / kernel acceptance etc.
CSVReporterAggregated() - Constructor for class CSVReporterAggregated
CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Outputs a CSV with statistics on the configuration/energy only the best configuration state changes.
CSVReporterBest() - Constructor for class CSVReporterBest
CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv: A row of the CSV File
CSVRow(ColumnDefinition) - Constructor for class CSVRow
CSVWriter - Class in org.anchoranalysis.io.generator.tabular
csvWriter(FeatureCSVMetadata) - Method in class FeatureExporterContext: Creates a FeatureCSVWriter for the non-aggregated results.
currentStateDescription() - Method in class ConcurrentJobMonitor
currentTemperature() - Method in class AnnealScheme
currentTemperature() - Method in class Geometry
currentTemperature() - Method in class NoAnnealing
customizeExperimentExecutor(ExperimentExecutor, CommandLine) - Method in class LauncherConfig
CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
CutBelowThreshold() - Constructor for class CutBelowThreshold
CVFindContours - Class in org.anchoranalysis.plugin.opencv: Wrapper around OpenCV's findContours function.
CVInit - Class in org.anchoranalysis.plugin.opencv: Provides for initialization of the JavaCPP bridge to OpenCV.

D

dataType() - Method in class ChannelFactorySingleType
dataType() - Method in class VoxelBuffer: Data-type of each voxel in the buffer.
dataType() - Method in interface VoxelsFactoryTypeBound: The data-type of the voxels, as created by this factory.
dataType() - Method in class Voxels: The underlying data-type of the voxels, represented by a VoxelDataType instance.
DataTypeMaxIntensity<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The maximum-intensity allowed by the data-type of the stack.
DataTypeMaxIntensity() - Constructor for class DataTypeMaxIntensity
DateStyle - Enum in org.anchoranalysis.plugin.io.naming.interval: How to style a date in a file-name.
DebugDependentProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes different processors depending on whether we are in debug mode or not.
DebugDependentProcessor() - Constructor for class DebugDependentProcessor
DebugModeParameters - Class in org.anchoranalysis.io.input.bean: An alternative mode of option where behaviours change.
DebugModeParameters(Optional<String>) - Constructor for class DebugModeParameters
decode(int) - Static method in class ChainCodesDirection: Decodes a chain-code into a point
decode(List<OnnxTensor>, ImageInferenceContext) - Method in class DecodeMaskRCNN
decode(List<OnnxTensor>, ImageInferenceContext) - Method in class DecodeEAST
decodeConnectedComponentID(int) - Method in class WatershedEncoding
DecodeEAST - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text: Extracts text from a RGB image by using the EAST deep neural network model and the ONNX Runtime.
DecodeEAST() - Constructor for class DecodeEAST
DecodeLabels<T> - Class in org.anchoranalysis.image.core.object.label: Decodes a labelled raster into derived objects or object-like elements.
DecodeLabels(Voxels<?>, int, int, DecodeLabels.CreateElementFromScaledObject<T>) - Constructor for class DecodeLabels
DecodeLabels.CreateElementFromScaledObject<T> - Interface in org.anchoranalysis.image.core.object.label: Creates an element from the scaled-object and its index.
DecodeMaskRCNN - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn: Decodes the inference output from a Mask-RCNN implementation.
DecodeMaskRCNN() - Constructor for class DecodeMaskRCNN
DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
DecomposeIntoConnectedComponents() - Constructor for class DecomposeIntoConnectedComponents
decrement() - Method in class Counter: Decreases the counter by one.
decrementX() - Method in class KernelPointCursor: Decrements the point and associated index by one in the X dimension.
decrementX() - Method in class Tuple3i: Decrements the X component's value by one.
decrementX(int) - Method in class Tuple3i: Decrements the X component's value by a shift.
decrementY() - Method in class KernelPointCursor: Decrements the point and associated index by one in the Y dimension.
decrementY() - Method in class Tuple3i: Decrements the Y component's value by one.
decrementY(int) - Method in class Tuple3i: Decrements the Y component's value by a shift.
decrementYTwice() - Method in class KernelPointCursor: Decrements the point and associated index by two in the Y dimension.
decrementZ() - Method in class KernelPointCursor: Decrements the point by one in the Z dimension.
decrementZ() - Method in class Tuple3i: Decrements the Z component's value by one.
decrementZ(int) - Method in class Tuple3i: Decrements the Z component's value by a shift.
deepCopy() - Method in class ColorList: Creates a new list, containing the duplicates of same elements as the current list.
deepCopy() - Method in class RandomCollectionWithAddCriteria
deepCopy() - Method in class EnergyTotal
deepCopy() - Method in class MarksWithEnergyBreakdown
deepCopy() - Method in class MarksWithTotalEnergy: Make a deep copy (except the energyScheme which is reused).
deepCopy() - Method in class VoxelizedMarksWithEnergy: Creates a deep-copy of the marks
deepCopy() - Method in class EnergySavedAll
deepCopy() - Method in class EnergySavedInd
deepCopy() - Method in class EnergySavedPairs
deepCopy() - Method in class ColoredMarks
deepCopy() - Method in class MarkCollection
deepCopy() - Method in class AggIDCounter
deepCopy() - Method in class Aggregator
Default - Class in org.anchoranalysis.io.bioformats.bean.options
Default() - Constructor for class Default
DEFAULT_CHARACTER - Static variable in class Divider: The default character used in the divider, if not otherwise specified in the constructor.
DEFAULT_COLOR_SET_GENERATOR - Static variable in class ColoredBase
DEFAULT_FUNC_NUM_PIXELS - Static variable in class MockFeatureWithCalculationFixture
DEFAULT_IMAGE_INPUT_NAME - Static variable in class MultiInput
DEFAULT_NUMBER_CHARACTERS_IN_BANNER - Static variable in class Divider: The default total nubmer of characters to use in the divier, if not otherwise specified in the constructor.
DefaultChildCacheFinder - Class in org.anchoranalysis.feature.session.cache.finder: The default strategy for finding children by always directly taking (or creating a child-cache) as necessary.
defaultColorIndexFor(int) - Method in class OutputWriteSettings
defaultExperimentOrCustom(CommandLine, Path) - Static method in class ExperimentFactory: Chooses either a path to the default-experiment or a path to a custom experiment.
DefaultInstance - Annotation Type in org.anchoranalysis.bean.annotation: Indicates a default bean-instance is available.
defaultOutputs() - Method in class InputOutputExperiment
defaultOutputs() - Method in class OutputExperiment: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class Task: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class SegmentIntoMarks: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class AggregateAnnotations
defaultOutputs() - Method in class CompareAnnotations
defaultOutputs() - Method in class ExportFeatures
defaultOutputs() - Method in class ConvertImageFormat
defaultOutputs() - Method in class ExportImageHistograms
defaultOutputs() - Method in class GroupedMeanChannelTask
defaultOutputs() - Method in class ImageAssignLabel
defaultOutputs() - Method in class ScaleImage
defaultOutputs() - Method in class SegmentInstanceWithModel
defaultOutputs() - Method in class ExtractSlice
defaultOutputs() - Method in class MovieFromSlices
defaultOutputs() - Method in class CombineCSV
defaultOutputs() - Method in class CopyFiles
defaultOutputs() - Method in class ConvertNamedChannels
defaultOutputs() - Method in class Develop
defaultOutputs() - Method in class ExportReportFeatures
defaultOutputs() - Method in class ExportObjectsAsCroppedImages
defaultOutputs() - Method in class ExportObjectsFromCSV
defaultOutputs() - Method in class SegmentMarksFromImage
defaultOutputs() - Method in class SegmentWithMarkedPointProcess
Define - Class in org.anchoranalysis.bean.define: A bean where the definitions of many different NamedBeans can be specified.
Define() - Constructor for class Define
Define<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Specifies a list of features directly without assigning any custom-naming.
Define(List<Feature<T>>) - Constructor for class Define
Define() - Constructor for class Define
DefineAdder - Interface in org.anchoranalysis.bean.define.adder: Indicates that an object can add one or more items to a Define.
DefineAdderBean - Class in org.anchoranalysis.bean.define.adder: Base class for AnchorBeans that can add items to a Define.
DefineAdderBean() - Constructor for class DefineAdderBean
DefineAdderWithPrefixBean - Class in org.anchoranalysis.bean.define.adder: Like DefineAdderBean but adds a prefix to the name of beans when adding.
DefineAdderWithPrefixBean() - Constructor for class DefineAdderWithPrefixBean
DefineAddException - Exception in org.anchoranalysis.bean.define: Called when a bean fails to be added to a Define.
DefineAddException(String) - Constructor for exception DefineAddException: Creates with a message only.
DefineAddException(Throwable) - Constructor for exception DefineAddException: Creates with a cause only.
DefineAddException(String, Throwable) - Constructor for exception DefineAddException: Creates with a message and cause.
DefinedNamed<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Specifies features via a list of names and associated with features.
DefinedNamed() - Constructor for class DefinedNamed
DefineFactory - Class in org.anchoranalysis.bean.define: Creates a new Define.
DefineFactory() - Constructor for class DefineFactory
DefineOutputter - Class in org.anchoranalysis.mpp.segment.bean.define: After using applying a Define on inputs, output produced entities (images, histograms, objects etc.)
DefineOutputter() - Constructor for class DefineOutputter
DefineOutputter.Processor<T> - Interface in org.anchoranalysis.mpp.segment.bean.define
DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define: Like a Define but outputs also an energy-stack.
DefineOutputterWithEnergy() - Constructor for class DefineOutputterWithEnergy
DefineOutputterWithEnergy.ProcessWithEnergyStack<T,S> - Interface in org.anchoranalysis.plugin.mpp.bean.define: Processes the energy-stack.
DefineSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Specifies a single feature directly without assigning any custom-naming.
DefineSingle() - Constructor for class DefineSingle
DefineSingle(Feature<T>) - Constructor for class DefineSingle
delegate() - Method in class ReadOptionsDelegate
delete(Path) - Method in interface AnnotationDeleter: Deletes all files at this path (or any other paths derived from this one.
delete(Path) - Method in class DualMarksAnnotationDeleter
delete(Path) - Method in class SimpleAnnotationDeleter
deriveBufferedImage() - Method in class DisplayStack: Derive a AWT BufferedImage from the DisplayStack after applying any applicable conversion.
deriveContext(InputOutputContext) - Method in class ExportFeaturesStyle
DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
DerivedObject() - Constructor for class DerivedObject
DeriveElementsFromSequencedDirectory<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced: Derives elements of type T from a directory containing a sequence of files.
DeriveElementsFromSequencedDirectory(SequencedDirectory) - Constructor for class DeriveElementsFromSequencedDirectory
deriveExtent() - Method in class ObjectCollectionProviderMorphological
deriveFrom(Supplier<Optional<Path>>, boolean) - Method in class DerivePath: Derives a new path from an existing path.
deriveFrom(Path, boolean) - Method in class DerivePath: Derives a new path from an existing path.
deriveFrom(Path, boolean) - Method in class Constant
deriveFrom(Path, boolean) - Method in class InsertRegExGroups
deriveFrom(Path, boolean) - Method in class JoinRegExGroups
deriveFrom(Path, boolean) - Method in class Replace
deriveFrom(Path, boolean) - Method in class Rooted
deriveFrom(Path, boolean) - Method in class CollapseFileName
deriveFrom(Path, boolean) - Method in class RemoveTrailingDirectory
deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class CalculateIntersecting
deriveFromDelegate(T, U) - Method in class CalculateInputFromDelegate
DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
DeriveFromPair() - Constructor for class DeriveFromPair
deriveIndex(String) - Static method in class RGBChannelNames: Derives the index of a channel for a channel name.
deriveInput(Stack, Optional<double[]>) - Method in class SegmentObjectsFromONNXModel
deriveInput(Stack, Optional<double[]>) - Method in class SegmentObjectsFromTensorFlowModel
deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, Logger) - Method in class CombineObjectsForFeatures: Derives a list of inputs (i.e.
deriveLabels(String, Optional<String>, int) - Method in interface LabelsForInput: Calculates labels for a given input (and index).
deriveName(File, FileNamerContext) - Method in class FileNamer: A name for a file.
deriveName(List<File>, FileNamerContext) - Method in class FileNamer: Derives a list of names (associated with each file) for some files.
deriveName(List<File>, FileNamerContext) - Method in class FileNamerIndependent
deriveName(File, Optional<Path>, int) - Method in class FileNamerIndependent
deriveName(File, Optional<Path>, int) - Method in class FromOutputName
deriveName(List<File>, FileNamerContext) - Method in class IfRelativeToDirectory
deriveName(File, Optional<Path>, int) - Method in class LastDirectories
deriveName(File, Optional<Path>, int) - Method in class NormalizedPath
deriveName(List<File>, FileNamerContext) - Method in class PatternSpan
deriveName(File, Optional<Path>, int) - Method in class RegExMatcher
deriveName(File, Optional<Path>, int) - Method in class RelativeToDirectory
deriveName(List<File>, FileNamerContext) - Method in class RemoveExtension
deriveName(List<File>, FileNamerContext) - Method in class SubsetRangeIfRequested
deriveNames() - Method in class FeatureList: Derives the names of the features.
deriveNameUnique(List<File>, FileNamerContext) - Method in class FileNamer: Like FileNamer.deriveName(List, FileNamerContext) but checks that the final list of named-files all have unique names.
deriveObject(BoundingBox) - Method in class PredicateAtCorner
deriveObject(BoundingBox) - Method in class PredicateImplementation
deriveObject(BoundingBox) - Method in interface VoxelsPredicate: Creates an object-mask for all the voxels inside the bounding-box satisfying the predicate.
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class Mark: Create a ObjectMask representation of the Mark.
deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class MarkCollection
DerivePath - Class in org.anchoranalysis.io.input.bean.path: Derives a path from an existing path.
DerivePath() - Constructor for class DerivePath
derivePath(DerivePath, Path) - Static method in class PathFromGenerator
DerivePathException - Exception in org.anchoranalysis.io.input.path
DerivePathException(String) - Constructor for exception DerivePathException
DerivePathException(Throwable) - Constructor for exception DerivePathException
DerivePathException(String, Throwable) - Constructor for exception DerivePathException
derivePointsLocal() - Method in class ObjectMask: Creates a list of all on voxels as points, using local coordinates i.e.
deriveRootedPath(Path, String, boolean, boolean) - Static method in class RootedFilePathUtilities
deriveRotationMatrix() - Method in class Orientation: Derives a RotationMatrix that can be applied to rotate an entity anti-clockwise to the current orientation.
deriveRotationMatrix() - Method in class Orientation2D
deriveRotationMatrix() - Method in class Orientation3DEulerAngles
deriveRotationMatrix() - Method in class OrientationAxisAngle
deriveRotationMatrix() - Method in class OrientationRotationMatrix
deriveScalingFactor(int, int) - Static method in class Scaler: Calculates a scaling-factor (for one dimension) by doing a floating point division of two integers.
deriveScore(double, double, FeatureResultSupplier) - Method in class GaussianCumulative
deriveScore(double, double, FeatureResultSupplier) - Method in class StatisticalBase: Derive scores given the value, mean and standard-deviation
deriveScore(double, double, FeatureResultSupplier) - Method in class ZScore
deriveScoreFromVoxel(int) - Method in class CalculateLevelBase
deriveScoreFromVoxel(int) - Method in class NormalizeByConstant
deriveScoreFromVoxel(int) - Method in class NormalizeByMax
deriveScoreFromVoxel(int) - Method in class SingleChannel
deriveStack(boolean) - Method in class DisplayStack: Derives a Stack from the display-stack that will be converted to 8-bit if necessary.
deriveStatistic(DoubleArrayList) - Method in class MeanAcrossObjects
deriveStatistic(DoubleArrayList) - Method in class ObjectAggregationBase
deriveStatistic(DoubleArrayList) - Method in class QuantileAcrossObjects
deriveSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class Outputter: Creates a new Outputter by appending a relative folder-path to the current Outputter
deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class OutputterChecked: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class ElementOutputter: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
deriveUnsignedBytePredicate() - Method in interface PredicateTwoBytes: Derives a predicate with a different interface for operating on UnsignedByteBuffer.
deriveUnsignedByteProcessor() - Method in interface PredicateTwoBytes: Derives a processor with a different interface for operating on UnsignedByteBuffer.
describe() - Method in class GraphWithoutPayload: Describes the graph in a multi-line string.
describe(boolean) - Method in class GraphWithPayload: Describes the graph in a multi-line string.
describe() - Method in interface SelectParam: A string that can be displayed to the user to describe this particular SelectParam.
describe() - Method in class UseDefaultManager
describe() - Method in class ProposerFailureDescription
describe() - Method in class DescribeGraph: Generates a string describing the entire graph (vertices and edges)
describe() - Method in class SummarizerImageMetadata
describe() - Method in class SummarizerInputFromManager
describe() - Method in class ExtensionCount
describe() - Method in class FilePathPattern
describe() - Method in class FileSizeStatistics
describe() - Method in class Summarizer: A string summarizing this item.
describe() - Method in class SummarizerAggregate
describe() - Method in class SummarizerCount
describe() - Method in class SummarizerListMultiline
describe() - Method in class SummarizerSplitMoreThan
describe(String) - Method in class FrequencyMap
describeAcceptedClasses() - Method in class AssignerMatchClass
describeAcceptedClasses() - Method in interface InitializationParameterAssigner: A string describing which classes of initialization-parameters are accepted or not.
describeBean() - Method in class AnchorBean: A (maybe longer) description identifying the bean and perhaps its key parameters.
describeBean() - Method in class Feature
describeBean() - Method in class FeatureList
describeBean() - Method in class Overlay
describeBean() - Method in class CombineRasterGenerator
describeBean() - Method in class BoundMinMax
describeBean() - Method in class BoundUnitless
describeBean() - Method in class BoundRotation2D
describeBean() - Method in class BoundRotation3D
describeBean() - Method in class MarkWithIdentifierFactory
describeBean() - Method in class AddCriteriaPair
describeBean() - Method in class MarkPairCollection
describeBean() - Method in class FeedbackReceiverList
describeBean() - Method in class FromMarkProposer
describeBean() - Method in class FromSerializedMarks
describeBean() - Method in class SimulatedAnnealing
describeChildren() - Method in class AnchorBean: Generates a string describing the children of the current bean.
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class DescribeGraph: Generates a string to describe a potential merge
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class GraphLogger
describeExecutionTimes(RunningSum, RecordedExecutionTimes, long) - Static method in class DescribeExecutionTimeStatistics: Describes how long operations took to complete en aggregate with related-statistics.
DescribeExecutionTimeStatistics - Class in org.anchoranalysis.experiment.time: Generates report of the execution-times of different operations.
DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge: Logs descriptions of the graph
DescribeGraph(NeighborGraph, boolean) - Constructor for class DescribeGraph: Constructor
describeLast() - Method in class Kernel
describeLast() - Method in class KernelBirth
describeLast() - Method in class KernelBirthAndKill
describeLast() - Method in class KernelDeath
describeLast() - Method in class KernelExchange
describeLast() - Method in class KernelInitialMarksFromPartition
describeLast() - Method in class KernelInitialMarksProposed
describeLast() - Method in class KernelInitialMarksVoxelized
describeLast() - Method in class KernelMerge
describeLast() - Method in class KernelReplace
describeLast() - Method in class KernelSplit
describeMarks(MarkCollection) - Method in class EnergySavedInd
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class DescribeGraph
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class GraphLogger
describeNoun() - Method in class BitDepth
describeNoun() - Method in class ImageSize
describeNoun() - Method in class NumberChannels
describeNoun() - Method in class SummarizerImageMetadata
describeOrientation(BiConsumer<String, String>) - Method in class Orientation: Consumes descriptive human-readable name-value pairs to describe the current orientation.
describeOrientation(BiConsumer<String, String>) - Method in class Orientation2D
describeOrientation(BiConsumer<String, String>) - Method in class Orientation3DEulerAngles
describeOrientation(BiConsumer<String, String>) - Method in class OrientationAxisAngle
describeOrientation(BiConsumer<String, String>) - Method in class OrientationRotationMatrix
describeParameters() - Method in class Feature: A human-readable description of the parameterization of the bean.
describeParameters() - Method in class Constant
describeParameters() - Method in class AsSingle
describeParameters() - Method in class ForSpecificAxis
describeParameters() - Method in class Count
describeParameters() - Method in class RatioThreshold
describeParameters() - Method in class BoundingBoxAlongAxisBase
describeParameters() - Method in class IntensityMeanShellBase
describeParameters() - Method in class UnitsWithinRange
describeParameters() - Method in class BoundingBoxExtent
describeParameters() - Method in class AsMark
describeParameters() - Method in class AsObject
describeParameters() - Method in class Intensity
describeParameters() - Method in class MeanIntensityDifference
describeParameters() - Method in class MaxOverlapRatio
describeParameters() - Method in class HOGFeature
describeParameters() - Method in class InvertedMax
describeParameters() - Method in class CompareWithRange
describeParameters() - Method in class CompareWithRangeFeature
describeParameters() - Method in class RangeCompareBase
describeParameters() - Method in class RangeCompareFromScalars
describeParameters() - Method in class StatisticalBase
describePropertiesFriendly() - Method in class MorphologicalIterations: A string that uniquely identifies all properties in the bean, but friendly to humans
describePropertyValue(T) - Method in class PermuteProperty: Describes a particular property-value in a unique but human-readable way.
describePropertyValue(Double) - Method in class PermutePropertyDoubleSet
describePropertyValue(Double) - Method in class PermutePropertySequenceDouble
describePropertyValue(Integer) - Method in class PermutePropertySequenceInteger
describePropertyValue(String) - Method in class PermutePropertyStringSet
describeTo(boolean) - Method in class TypedEdge: Describes the edge by showing the to vertex, and optionally the payload.
description() - Method in class MutableDirectory: A description of this directory for the manifest.
description(String, String) - Static method in class DirectoryMatch
description(String, String) - Static method in class FileMatch: Match a file whose manifest-description has a specific function and type.
description(String) - Static method in class FileMatch: Match a file whose manifest-description has a specific function.
description(String, String, String) - Static method in class FileMatch: Match a file whose manifest-description has either of two specific function and a specific type.
descriptionAndOutputName(String, String, String, String) - Static method in class FileMatch: Match a file whose manifest-description has either of two specific function and a specific type and whose output-name matches a specific value.
descriptionForList(String) - Method in class FeatureFromList: Derive a string description of all the items of the list concatenated together.
descriptionLong() - Method in class Feature: A long human-readable description of the feature and some or all of its parameterization.
descriptionLong() - Method in class Constant
descriptionLong() - Method in class Reference
descriptionLong() - Method in class Sum
descriptionLong() - Method in class Intensity
descriptionLong() - Method in class AbsoluteValue
descriptionLong() - Method in class Divide
descriptionLong() - Method in class InvertedMax
descriptionLong() - Method in class Multiply
descriptionLong() - Method in class MeanGeometric
descriptionLong() - Method in class NormalizedRange
descriptionLong() - Method in class Range
descriptionLong() - Method in class WithValueBase
DescriptionMatch - Class in org.anchoranalysis.io.manifest.finder.match
descriptiveIdentifier() - Method in interface FileFormat: An identifier that describes the format, that is meaningful to the end-user.
descriptiveIdentifier() - Method in enum ImageFileFormat
descriptiveIdentifier() - Method in enum NonImageFileFormat
DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
DescriptiveNameContainsImageLabeller() - Constructor for class DescriptiveNameContainsImageLabeller
DeserializationFailedException - Exception in org.anchoranalysis.core.serialize: When a deserialization operation fails.
DeserializationFailedException(String) - Constructor for exception DeserializationFailedException: Creates with a message, but without a cause.
DeserializationFailedException(Exception) - Constructor for exception DeserializationFailedException: Creates with a cause, but without a message.
DeserializationFailedException(String, Throwable) - Constructor for exception DeserializationFailedException: Creates with message and cause.
deserialize(Path, Logger) - Method in interface Deserializer: Deserializes a representation of an object stored on the filesystem.
deserialize(Path, Logger) - Method in class DictionaryDeserializer
deserialize(Path, Logger) - Method in class ObjectInputStreamDeserializer
deserialize(Path, Logger) - Method in class XStreamDeserializer
deserialize(Path, Logger) - Method in class MarkCollectionDeserializer
DeserializedManifest - Class in org.anchoranalysis.plugin.io.manifest: A manifest after being deserialized from the file-system.
DeserializedManifest(File, ManifestDeserializer, Logger) - Constructor for class DeserializedManifest
deserializeManifest(File, Logger) - Method in interface ManifestDeserializer
deserializeManifest(File, Logger) - Method in class SimpleManifestDeserializer
Deserializer<T> - Interface in org.anchoranalysis.core.serialize: Creates an object from a serialized representation on the file-system.
DestinationChannelForIndex - Interface in org.anchoranalysis.io.bioformats: Selects a destination-channel for the byte-copier, given an index
destinationPath(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class CopyFilesNaming: Returns the output path (destination to to be copied to) for a given single file.
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<AnonymizeSharedState>) - Method in class Anonymize
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<ClusterMembership>) - Method in class ClusterByTimestamp
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class CopyFilesNaming: Calculates the relative-output path (to be appended to destDir)
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class CopyFilesNamingOne
destinationPathRelative(Path) - Method in class CopyFilesNamingOne
destinationPathRelative(Path, String) - Method in class FilterWithRegularExpression
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class OutputPrefixWithExtension
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class PreserveName
destinationPathRelative(Path) - Method in class RegularExpressionBase
destinationPathRelative(Path, String) - Method in class RegularExpressionBase
destinationPathRelative(Path) - Method in class RemoveWhitespace
destinationPathRelative(Path, String) - Method in class SubstituteRegularExpression
destinationSize - Variable in class ConvertTo: The total number of elements (whatever the destination type is) in the destination buffer.
determineChannelNames(IFormatReader) - Method in class Default
determineChannelNames(IFormatReader) - Method in class ReadOptions: A list of channel-names, if available.
determineChannelNames(IFormatReader) - Method in class ReadOptionsDelegate
determineChannelNames(IFormatReader) - Method in class SwitchChannelTime
determineCost() - Method in class MergeCandidate: Merges
determineEnabledOutputs(RecordedOutputsWithRules) - Method in class OutputManager: Determines which outputs are enabled or not.
determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType: Finds a common input-type for two classes, throwing an exception if the two types aren't compatible.
determineInputType(List<Feature<T>>) - Static method in class FeatureInputType: Finds a common input-type for classes in the list, throwing an exception if any two types aren't compatible.
determineOrientationCorrection(Path) - Static method in class OrientationReader: Determines the needed correction to orientation for the voxels if an EXIF orientation tag is present.
determineOrientationCorrection(Metadata) - Static method in class OrientationReader: Determines the needed correction to orientation for the voxels if an EXIF orientation tag is present.
Develop - Class in org.anchoranalysis.plugin.mpp.experiment.bean.define: Derives various types of outputs (images, histograms etc.) from MultiInputs.
Develop() - Constructor for class Develop
dictionaries() - Method in class ImageInitialization
Dictionary - Class in org.anchoranalysis.core.value: Collection of parameters represented by key-value pairs.
Dictionary() - Constructor for class Dictionary: Creates empty, with no parameters.
dictionary() - Method in class MarksInitialization
dictionary() - Method in class MultiInput
DICTIONARY_IDENTIFIER - Static variable in class ImageInitialization
DictionaryBean<T> - Class in org.anchoranalysis.bean.shared.dictionary: Base class for beans that require initialization with DictionaryInitialization.
DictionaryBean() - Constructor for class DictionaryBean
DictionaryCondition - Class in org.anchoranalysis.plugin.image.bean.dictionary: Checks if a value in a Dictionary is equal to an expected-value.
DictionaryCondition() - Constructor for class DictionaryCondition
dictionaryDeriver() - Method in class MarkProposerStrategy
DictionaryDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes a Dictionary from a file-system representation as a Java properties file.
DictionaryDeserializer() - Constructor for class DictionaryDeserializer
DictionaryForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme: Creates a Dictionary for a particular EnergyStack that is associated with a EnergyScheme
DictionaryForImageCreator(EnergyScheme, SharedFeatures, Logger) - Constructor for class DictionaryForImageCreator
DictionaryGenerator - Class in org.anchoranalysis.io.generator.serialized: Writes the contents of a Dictionary to the file-system as XML.
DictionaryGenerator(String) - Constructor for class DictionaryGenerator
DictionaryInitialization - Class in org.anchoranalysis.bean.shared.dictionary: Initialization parameters that provide a named-mapping to Dictionarys.
DictionaryInitialization(SharedObjects) - Constructor for class DictionaryInitialization: Creates using a SharedObjects to create a NamedProviderStore for the dictionaries.
dictionaryInitialization() - Method in class ImageInitialization
DictionaryProvider - Class in org.anchoranalysis.bean.shared.dictionary: Base class for beans that implement Provider to provide a Dictionary.
DictionaryProvider() - Constructor for class DictionaryProvider
DictionaryProviderReference - Class in org.anchoranalysis.bean.shared.dictionary: References a particular Dictionary in shared-object-space.
DictionaryProviderReference() - Constructor for class DictionaryProviderReference
Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
Difference() - Constructor for class Difference
DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score: Similar to Difference but calculates the width as the standard-deviation of the histogram
DifferenceCalculateLevelStandardDeviation() - Constructor for class DifferenceCalculateLevelStandardDeviation
differenceFrom(Path, Path) - Static method in class PathDifference: Finds the difference between a path and a base.
dilate(boolean, Optional<Extent>) - Method in class BoundedVoxels: Grow bounding-box by 1 pixel in all directions.
dilate(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class MorphologicalDilation: Dilates an ObjectMask, growing the bounding-box as necessary.
dilate(BinaryVoxels<UnsignedByteBuffer>, int, DilationContext) - Static method in class MorphologicalDilation: Performs a morphological dilation operation.
Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs a dilation morphological operation on BinaryVoxels.
Dilate() - Constructor for class Dilate
Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Dilate() - Constructor for class Dilate
DilationContext - Class in org.anchoranalysis.image.voxel.kernel.morphological: Additional parameters for influencing a morphologicla dilation opperation.
DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>) - Constructor for class DilationContext: Create without a post-condition.
DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>, Optional<AcceptIterationPredicate>) - Constructor for class DilationContext: Create with a post-condition.
DilationKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological: Morphological dilation with a 3x3 or 3x3x3 kernel size.
DilationKernel(boolean) - Constructor for class DilationKernel: Creates with a type of neighborhood.
dimensionIndexFor(Axis) - Static method in class AxisConverter: A corresponding index representing for the dimension an Axis represents.
dimensions() - Method in class EnergyStack: The image-dimensions associated with the energy-stack.
dimensions() - Method in class EnergyStackWithoutParameters: The dimensions of all channels in the stack.
dimensions() - Method in class FeatureInputDimensions: The dimensions of the associated image.
dimensions() - Method in class FeatureInputEnergy
dimensions() - Method in class Channel: The size and voxel-resolution of the channel.
Dimensions - Class in org.anchoranalysis.image.core.dimensions: The size of an image (in voxels), together with the image resolution.
Dimensions(int, int, int) - Constructor for class Dimensions: Construct with an explicit extent and no resolution.
Dimensions(ReadableTuple3i) - Constructor for class Dimensions: Construct with an explicit extent and no resolution.
Dimensions(Extent) - Constructor for class Dimensions: Construct with an explicit extent and no resolution.
Dimensions(Extent, Optional<Resolution>) - Constructor for class Dimensions
dimensions(Dimensions) - Method in enum OrientationChange: A Dimensions that describes {code dimensions} after the orientation change.
dimensions() - Method in class Mask: The size and voxel-resolution of the channel.
dimensions() - Method in class DisplayStack: The dimensions of all channels in the stack.
dimensions() - Method in class RGBStack: The dimensions of all channels in the stack.
dimensions() - Method in class Stack: The dimensions of all channels in the stack.
dimensions() - Method in class FeatureInputImageMetadata
dimensions(int, Logger) - Method in class NamedChannelsInput: Dimensions of a particular series.
dimensions(Logger) - Method in interface NamedChannelsForSeries
dimensions(Logger) - Method in class NamedChannelsForSeriesConcatenate
dimensions(Logger) - Method in class NamedChannelsForSeriesMap
dimensions() - Method in class ObjectsAsGrayscaleGenerator: The dimensions associated with the objects (assumed to be constant across any change in element).
dimensions() - Method in class TimeSequence
dimensions() - Method in class FeatureInputMarkCollection
dimensions() - Method in class ProposerContext
dimensions() - Method in class TransformationContext
DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel
DimensionsCreator - Class in org.anchoranalysis.io.bioformats
DimensionsCreator(IMetadata) - Constructor for class DimensionsCreator
dimensionsForSeries(int, Logger) - Method in interface OpenedImageFile: The Dimensions associated with a particular series.
dimensionsForSeries(int, Logger) - Method in class OpenedMultiFile
dimensionsOptional() - Method in class FeatureInputEnergy: The image-dimensions associated with the energy-stack, if it exists.
DimensionsProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide Dimensions.
DimensionsProvider() - Constructor for class DimensionsProvider
dimensionsRequired() - Method in class FeatureInputEnergy: The image-dimensions associated with the energy-stack, or an exception if no energy-stack exists.
DirectAssignMode<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: Directly assigns a state for every optimisation step
DirectAssignMode() - Constructor for class DirectAssignMode
DirectAssignMode(ExtractScoreSize<S>) - Constructor for class DirectAssignMode
DirectionVector - Class in org.anchoranalysis.spatial.orientation: A vector indicating a direction in space.
DirectionVector() - Constructor for class DirectionVector: Creates with each dimension's value set to 0.
DirectionVector(Tuple3d) - Constructor for class DirectionVector: Creates reusing Tuple3d internally for the dimension's values.
DirectionVector(double, double, double) - Constructor for class DirectionVector: Creates for a particular value in each dimension.
DirectionVector(Axis) - Constructor for class DirectionVector: Creates a direction aligned to a particular axis.
DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction: A bean that creates a DirectionVector
DirectionVectorBean() - Constructor for class DirectionVectorBean
directory() - Method in class InputsWithDirectory: The directory associated with the inputs.
DirectoryCreator - Class in org.anchoranalysis.core.system.path: Creates necessary directories on a file-system to make a path valid.
DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider: Lists all directories to a certain depth
DirectoryDepth() - Constructor for class DirectoryDepth
DirectoryMatch - Class in org.anchoranalysis.io.manifest.finder.match
DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Reuses the directories between a path and its root to form the output - and also the filename.
DirectoryStructure() - Constructor for class DirectoryStructure
DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer
DirectoryWithPrefix(Path) - Constructor for class DirectoryWithPrefix
DirectoryWithPrefix(Path, String, String) - Constructor for class DirectoryWithPrefix
disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta: Assigns additional outputs to disable.
DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective: Calculates features values for all objects, and discards any object less than quantile - (minRatio * stdDev)
DiscardOutliers() - Constructor for class DiscardOutliers
DisplayStack - Class in org.anchoranalysis.image.core.stack: Stack that contains 1 or 3 channels so that we and display it as either grayscale or as an RGB unsigned 8-bit image, respectively.
DisplayStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Writes a display-stack to the filesystem.
DisplayStackGenerator(String, boolean) - Constructor for class DisplayStackGenerator: Creates the generator.
distance(BoundingBox, BoundingBox, boolean) - Static method in class BoundingBoxDistance: Calculates the distance between two BoundingBoxes.
distance(Point2d) - Method in class Point2d: The square of the Euclidean distance between this point and another Point2d.
distance(Point3d) - Method in class Point3d: The Euclidean distance between this point and another Point3d.
distance(Point3f) - Method in class Point3f: The Euclidean distance between this point and another.
distance(Point3i) - Method in class Point3i: The Euclidean distance between this point and another.
DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class DistanceCondition
DistanceIndex - Class in org.anchoranalysis.plugin.mpp.contour.distance: A distance, and the index the point came from
DistanceIndex(int, int) - Constructor for class DistanceIndex
DistanceIndexTwice - Class in org.anchoranalysis.plugin.mpp.contour.distance: A distance, and the two indices the point came from
DistanceIndexTwice(int, int, int) - Constructor for class DistanceIndexTwice
distanceMax(Point3i) - Method in class Point3i: The maximum distance across any individual axis to another point.
DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance
DistancePhysical() - Constructor for class DistancePhysical
distanceSquared(Point2d) - Method in class Point2d: The square of the Euclidean distance between this point and another Point2d.
distanceSquared(Point3d) - Method in class Point3d: The square of the Euclidean distance between this point and another Point3d.
distanceSquared(Point3i) - Method in class Point3d: The square of the Euclidean distance between this point and another Point3i.
distanceSquared(Point3f) - Method in class Point3f: The square of the Euclidean distance between this point and another.
distanceSquared(Point3i) - Method in class Point3i: The square of the Euclidean distance between this point and another Point3i.
distanceSquared(Point3d) - Method in class Point3i: The square of the Euclidean distance between this point and another Point3d.
distanceSquaredTo(Point3i) - Method in class LevelResult
DistanceToContiguousPath - Class in org.anchoranalysis.plugin.mpp.contour.distance
DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
DistanceTransform3D() - Constructor for class DistanceTransform3D
DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Like DistanceTransform3D but applies the distance transform separately for each object in a collection.
DistanceTransformForEachObject3D() - Constructor for class DistanceTransformForEachObject3D
DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance
DistanceVoxels(double) - Constructor for class DistanceVoxels
DistanceVoxels() - Constructor for class DistanceVoxels
div(int) - Method in class AggIDCounter
div(AggIDCounter) - Method in class AggIDCounter
Divide<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Divide() - Constructor for class Divide
divideBy(int) - Method in interface VoxelsArithmetic: Divides the value of all voxels by a scalar constant.
divideBy(int) - Method in class Aggregator
divideBy(int) - Method in class Tuple3d: Arithmetically divide values across each dimension.
divideBy(double) - Method in class Tuple3d: Arithmetically divide values across each dimension.
divideBy(int) - Method in class Tuple3i: Arithmetically divide by a value across each dimension.
DivideByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
DivideByConstant() - Constructor for class DivideByConstant
divideByZeroReplace(double, double, double) - Static method in class DoubleUtilities: Replaces a value with a constant if the denominator is 0.
Divider - Class in org.anchoranalysis.core.log: Creates a line of text that span a certain width with a repeated character, optionally containing a label.
Divider() - Constructor for class Divider: A banner using dashes.
Divider(int) - Constructor for class Divider: A banner using dashes, with a particular number of characters.
Divider(char) - Constructor for class Divider: A banner using a particular repeated character.
Divider(char, int) - Constructor for class Divider: A banner using a particular repeated character.
doDuplicate(PointListBase) - Method in class PointListBase
doesClassInheritFromAny(Class<? extends InputFromManager>) - Method in class InputTypesExpected: Does the childclass inherit from any one of expected input-types
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class BinaryKernelMorphological: Does a particular neighboring-point satisfy the conditions.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class DilationKernel
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class ErosionKernel: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class OutlineKernel: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class OutlineKernelNeighborMatchValue: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborVoxelQualify(Point3i) - Method in class CountKernel: Whether a particular neighboring voxel is accepted or not.
doesNeighborVoxelQualify(Point3i) - Method in class CountKernelNeighborhood
doesNeighborVoxelQualify(Point3i) - Method in class CountKernelNeighborhoodMask
doesPathExist(String) - Method in class TestLoader: Does a resource exist with a particular folderPath + fileName.
doesPathExist(String, String) - Method in class TestLoader: Does a resource exist with a particular folderPath + fileName.
doFind(Manifest) - Method in interface Finder
doFind(Manifest) - Method in class FinderExperimentFileDirectories
doFind(Manifest) - Method in class FinderSingleDirectory
doFind(Manifest) - Method in class FinderSingleFile
doJobOnInput(InputBound<T, S>) - Method in class Task: Performs the task on a particular input.
doJobOnInput(InputBound<S, NoSharedState>) - Method in class HelloWorld
doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class AggregateAnnotations
doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, ComparisonSharedState<T>>) - Method in class CompareAnnotations
doJobOnInput(InputBound<T, FeatureExporter<S>>) - Method in class ExportFeatures
doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class GroupedStackBase
doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class ImageAssignLabel
doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class RasterTask
doJobOnInput(InputBound<StackSequenceInput, NoSharedState>) - Method in class ScaleImage
doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class SegmentInstanceWithModel
doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class ExtractSlice
doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class CombineCSV
doJobOnInput(InputBound<FileWithDirectoryInput, RecordingCounter<T>>) - Method in class CopyFiles
doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class SummarizeBase
doJobOnInput(InputBound<T, SharedStateRememberConverted<U, S>>) - Method in class ConvertNamedChannels
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class Develop
doJobOnInput(InputBound<ManifestCouplingDefinition, NoSharedState>) - Method in class ExportReportFeaturesFromManifest
doJobOnInput(InputBound<MultiInput, CSVWriter>) - Method in class ExportReportFeaturesFromMulti
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class ExportObjectsAsCroppedImages
doJobOnInput(InputBound<FromCSVInput, FromCSVSharedState>) - Method in class ExportObjectsFromCSV
doJobOnInput(InputBound<MultiInput, ExperimentState>) - Method in class SegmentMarksFromImage
doOperation(VoxelizedMarkMemo, Dimensions) - Method in class PxlListOperationFromMark
doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class ConvertImageFormat
doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class RasterTask: Processes one stack from a series.
doStack(InputBound<NamedChannelsInput, OutputSequenceIncrementing<Stack>>, NoSharedState, int, int, InputOutputContext) - Method in class MovieFromSlices
dotProduct(Tuple3d) - Method in class Tuple3d: Computes the dot-product of the tuple with another.
DotProductOrientationToVector - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
DotProductOrientationToVector() - Constructor for class DotProductOrientationToVector
double3DFromFloat(Point2f) - Static method in class PointConverter: Convert a Point2f to a Point3d.
DoubleBiPredicate - Interface in org.anchoranalysis.math.relation: Like BiPredicate but operates on doubles.
doubleFromFloat(Point2f) - Static method in class PointConverter: Convert a Point2f to a Point2d.
doubleFromFloat(Point3f) - Static method in class PointConverter: Convert a Point3f to a Point3d.
doubleFromInt(Point2i) - Static method in class PointConverter: Convert a Point2i to a Point3d using 0 as the value of the Z-axis component.
doubleFromInt(ReadableTuple3i) - Static method in class PointConverter: Convert a ReadableTuple3i to a Point3d.
DoubleList - Class in org.anchoranalysis.bean.primitive: A bean defining a list of Doubles.
DoubleList(Double...) - Constructor for class DoubleList: Constructs with one or more values added to the list.
DoubleListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a DoubleList from a XML element.
DoubleListFactory() - Constructor for class DoubleListFactory
DoubleSet - Class in org.anchoranalysis.bean.primitive: A bean defining a set of Doubles.
DoubleSet(Double...) - Constructor for class DoubleSet: Constructs with one or more values added to the set.
DoubleSet() - Constructor for class DoubleSet
DoubleSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a DoubleSet from a XML element.
DoubleSetFactory() - Constructor for class DoubleSetFactory
DoubleUtilities - Class in org.anchoranalysis.math.arithmetic: Utilities for arithmetic operations involving type double.
DrawColoredObjects - Class in org.anchoranalysis.annotation.io.assignment.generator: Outlines or completely fills in each ObjectMask with a color.
DrawColoredObjects(DisplayStack, boolean, int) - Constructor for class DrawColoredObjects
DrawCroppedObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: Similar to DrawObjectsGenerator
DrawCroppedObjectsGenerator(DrawObject, DisplayStack, ColorIndex) - Constructor for class DrawCroppedObjectsGenerator
DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider: Draws a lines between successive points on the convex-hull of an object.
DrawLineAlongConvexHull() - Constructor for class DrawLineAlongConvexHull
DrawObject - Class in org.anchoranalysis.overlay.bean: Draws an object-mask on a RGB-stack
DrawObject() - Constructor for class DrawObject
DrawObjectOnStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box: Creates images of object(s) drawn on a background only in a local region around their bounding box.
DrawObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: Generates stacks of RGB images using a DrawObject to draw objects on a background.
DrawOverlay - Class in org.anchoranalysis.overlay.writer: Draws an overlay onto a RGB-stack, including precalculated overlays.
DrawOverlay() - Constructor for class DrawOverlay
dropKey() - Method in exception NamedFeatureCalculateException: Removes any feature-name from the exception.
dropZ() - Method in class Point3d: Creates a new point with identical x and y values, but with z set to 0.
DualMarks - Interface in org.anchoranalysis.annotation.mark: Two mark-collections, one considered accepted and the other rejected.
DualMarksAnnotation<T> - Class in org.anchoranalysis.annotation.mark: An annotation that consists of two sets of marks, accepted and rejected.
DualMarksAnnotation() - Constructor for class DualMarksAnnotation
DualMarksAnnotationAsObjects<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer: Loads a DualMarksAnnotation to compared, converting each Mark into an ObjectMask.
DualMarksAnnotationAsObjects() - Constructor for class DualMarksAnnotationAsObjects
DualMarksAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark: Deletes DualMarksAnnotations from the file-system.
DualMarksAnnotationDeleter() - Constructor for class DualMarksAnnotationDeleter
DualMarksAnnotationReader<T> - Class in org.anchoranalysis.annotation.io.mark: Reads DualMarksAnnotations from the file-system.
DualMarksAnnotationReader(boolean) - Constructor for class DualMarksAnnotationReader
DualMarksAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark: Writes DualMarksAnnotations to the file-system.
DualMarksAnnotationWriter() - Constructor for class DualMarksAnnotationWriter
DualMarksAnnotationWriter(boolean) - Constructor for class DualMarksAnnotationWriter
DualPathPredicates - Class in org.anchoranalysis.io.input.path.matcher: A Predicate<Path for both a file and a directory.
DualPathPredicates(Predicate<Path>, Predicate<Path>) - Constructor for class DualPathPredicates
DualStack - Class in org.anchoranalysis.mpp.segment.optimization: Stores an EnergyStack together with a background stack.
DualStack(EnergyStack) - Constructor for class DualStack: Creates to infer a background from the energy-stack.
DualStack(EnergyStack, DisplayStack) - Constructor for class DualStack
DualState<T> - Class in org.anchoranalysis.mpp.segment.optimization: Remembers the current state of type T and some best state (which was once set from the current state)
DualState() - Constructor for class DualState
DualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization: A transformation of one VoxelizedMarksWithEnergy into another
DualVoxelizedMarks(VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Constructor for class DualVoxelizedMarks
DualWriterOperationRecorder - Class in org.anchoranalysis.io.manifest.operationrecorder: Allows two WriteOperationRecorder function together as if they are one
DualWriterOperationRecorder(WriteOperationRecorder, WriteOperationRecorder) - Constructor for class DualWriterOperationRecorder
duplicate() - Method in class RGBColor: Creates a deep-copy of the current object.
duplicate() - Method in class Dictionary: Deep-copy of existing dictionary.
duplicate() - Method in class SharedFeatures: A deep copy of the current instance.
duplicate() - Method in class NamedFeatureStore: Deep-copies the store, including duplicating each feature.
duplicate() - Method in class Channel: A deep-copy.
duplicate() - Method in class Mask: Deep-copies the object.
duplicate() - Method in class ObjectWithProperties: Deep copies the current instance.
duplicate() - Method in class RGBStack: A deep copy.
duplicate() - Method in class StackNotUniformSized: A deep-copy.
duplicate() - Method in class MergedPairsFeatures: Immutably creates entirely new duplicated features
duplicate() - Method in class BinaryVoxels: Deep-copy of the object, including duplicating voxel buffers in memory.
duplicate() - Method in class BoundedVoxels: A deep-copy of the current structure.
duplicate() - Method in class VoxelBuffer: Creates a deep copy of the current object, including deep-copying the associated buffer.
duplicate() - Method in class ObjectCollection: Deep copy, including duplicating ObjectMasks.
duplicate() - Method in class ObjectMask: Creates a deep-copy of the current object-mask.
duplicate() - Method in class Voxels: A deep-copy.
duplicate() - Method in class IndexableOutputNameStyle
duplicate() - Method in class IntegerSuffixOutputNameStyle
duplicate() - Method in class OutputNameStyle: Deep copy the current object.
duplicate() - Method in class SimpleOutputNameStyle
duplicate() - Method in class StringSuffixOutputNameStyle
duplicate() - Method in class WithoutOutputNameStyle
duplicate() - Method in class RunningSum: Deep-copy.
duplicate() - Method in class Histogram: Creates a deep-copy of the current object.
duplicate() - Method in class EigenvalueAndVector: Creates a deep-copy of the current object.
duplicate() - Method in class ImageMoments: Creates a deep-copy of the current object.
duplicate() - Method in class Bound
duplicate() - Method in class BoundDegrees
duplicate() - Method in class BoundPhysicalExtent
duplicate() - Method in class BoundUnitless
duplicate() - Method in class Circle
duplicate() - Method in class Ellipse
duplicate() - Method in class Ellipsoid
duplicate() - Method in class Sphere
duplicate() - Method in class Mark
duplicate() - Method in class LineSegment
duplicate() - Method in class PointList
duplicate() - Method in class Polygon
duplicate() - Method in class PolygonCurve
duplicate() - Method in class RotatableBoundingBox
duplicate() - Method in interface VoxelizedMark
duplicate() - Method in class AxisLimits
Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Duplicate() - Constructor for class Duplicate
Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider
Duplicate() - Constructor for class Duplicate
Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider: Duplicates (deep copy) an object-collection.
Duplicate() - Constructor for class Duplicate
duplicate() - Method in class ContiguousVoxelPath
duplicate() - Method in class RotationMatrix: Deep-copy of the current rotation-matrix.
duplicateBean() - Method in class AnchorBean: Creates a new bean that deep-copies every property value.
duplicateBean() - Method in class Define
duplicateBean() - Method in class DoubleList: Duplicate the bean.
duplicateBean() - Method in class DoubleSet: Duplicate the bean.
duplicateBean() - Method in class IntegerList: Duplicate the bean.
duplicateBean() - Method in class IntegerSet: Duplicate the bean.
duplicateBean() - Method in class StringList: Duplicate the bean.
duplicateBean() - Method in class StringSet: Duplicate the bean.
duplicateBean() - Method in class RGBColorBean
duplicateChangeExtent(Extent) - Method in class Dimensions: Deep-copies the current object, but assigns a different Extent.
duplicateChangeName(String) - Method in class Feature: Duplicates the feature as per AnchorBean.duplicateBean() but sets a particular custom-name.
duplicateChangeResolution(Optional<Resolution>) - Method in class Dimensions: Deep-copies the current object, but assigns a different Resolution.
duplicateChangeZ(int) - Method in class Dimensions: Deep-copies the current object, but assigns a different size for the Z-dimension.
duplicateChangeZ(int) - Method in class Extent: Creates a copy of the current Extent with the value for the Z-dimension changed.
duplicateChangeZ(int) - Method in class Point3i
duplicateChangeZ(int) - Method in interface ReadableTuple3i: Creates a copy of the current tuple, but with a different Z-component value.
duplicateDeep() - Method in class Stack: Performs a deep copy of the stack, so that all channels are duplicated.
duplicateForNewThread() - Method in interface FeatureTableCalculator: Makes a copy of the feature-store for a new thread.
duplicateForNewThread() - Method in class PairsTableCalculator
duplicateForNewThread() - Method in class SingleTableCalculator
duplicateFresh() - Method in class VoxelizedMarkMemo
duplicateShallow() - Method in class FeatureInitialization: A shallow-copy of the current initialization.
duplicateShallow() - Method in class FeatureNameList: Shallow copy of the current instance.
duplicateShallow() - Method in class Stack: Performs a shallow copy of the stack, so that all channels are reused.
duplicateShallow() - Method in class ObjectCollection: Shallow copy of objects.

E

EachObjectIndependently - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Simply selects features directly from the list, and objects directly from the list passed.
EachObjectIndependently() - Constructor for class EachObjectIndependently
EagerEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store: Evaluates items immediately via the StoreSupplier as soon as they are added.
EagerEvaluationStore() - Constructor for class EagerEvaluationStore
EccentricityAxisAligned - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
EccentricityAxisAligned() - Constructor for class EccentricityAxisAligned
EdgeFilterIJ - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
EdgeFilterIJ() - Constructor for class EdgeFilterIJ
edgesMaybeDuplicates() - Method in class GraphWithPayload: The edges in the graph, all of them, but with some edges possibly duplicated.
edgesUnique() - Method in class GraphWithPayload: The edges in the graph, all of them, without any duplicates.
effectiveBitsPerPixel(IFormatReader) - Method in class Default
effectiveBitsPerPixel(IFormatReader) - Method in class ReadOptions: The number of bits used per pixel.
effectiveBitsPerPixel(IFormatReader) - Method in class ReadOptionsDelegate
EigenvalueAndVector - Class in org.anchoranalysis.math.statistics.moment: An eigenvalue and its corresponding eigenvector.
EigenvalueAndVector(double, DoubleMatrix1D) - Constructor for class EigenvalueAndVector
eitherFunctionAndType(String, String, String) - Static method in class DescriptionMatch
ElementOutputter - Class in org.anchoranalysis.io.output.writer: Outputs an element to the file-system.
ElementOutputter(OutputterChecked, ExecutionTimeRecorder, Supplier<Optional<Logger>>) - Constructor for class ElementOutputter
elementRange() - Method in class IncreasingIntegers
elementRange() - Method in class IncrementingIntegers
elementRange() - Method in class SequenceType
elementRange() - Method in class StringsWithoutOrder
ElementSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element to output files together with a ElementWriter.
elementwiseOperation(ReadableTuple3i, ReadableTuple3i, IntBinaryOperator) - Static method in class Point3i: Creates a new point by applying a pairwise operation to each dimension's values for two tuples.
ElementWriter<T> - Interface in org.anchoranalysis.io.output.writer: Writes an element (with or without an index) to the file system.
ElementWriterSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element-writer to output files.
Ellipse - Class in org.anchoranalysis.mpp.mark.conic
Ellipse() - Constructor for class Ellipse
Ellipse(Ellipse) - Constructor for class Ellipse
EllipseStandardFormConverter - Class in org.anchoranalysis.plugin.points.bean.fitter
EllipseStandardFormConverter(DoubleMatrix1D) - Constructor for class EllipseStandardFormConverter
Ellipsoid - Class in org.anchoranalysis.mpp.mark.conic
Ellipsoid() - Constructor for class Ellipsoid
Ellipsoid(Ellipsoid) - Constructor for class Ellipsoid
EllipsoidAxisRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
EllipsoidAxisRatio() - Constructor for class EllipsoidAxisRatio
EllipsoidBase - Class in org.anchoranalysis.plugin.points.bean.feature
EllipsoidBase() - Constructor for class EllipsoidBase
EllipsoidFactory - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
EllipsoidFitHelper - Class in org.anchoranalysis.plugin.points.bean.fitter
Ellipsoidicity - Class in org.anchoranalysis.plugin.points.bean.feature
Ellipsoidicity() - Constructor for class Ellipsoidicity
EllipsoidMaxAreaIntersectingPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
EllipsoidMaxAreaIntersectingPlane() - Constructor for class EllipsoidMaxAreaIntersectingPlane
EllipsoidUtilities - Class in org.anchoranalysis.mpp.mark.conic
Ellipticity - Class in org.anchoranalysis.plugin.points.bean.feature
Ellipticity() - Constructor for class Ellipticity
empty() - Static method in class FeatureListFactory: Creates an empty list of features
empty() - Static method in class ObjectCollectionFactory: Creates a newly created object-collection that is empty.
Empty - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates an empty object-collection.
Empty() - Constructor for class Empty
EmptyHistogramConstant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Specifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
EmptyHistogramConstant() - Constructor for class EmptyHistogramConstant
enableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta: Assigns additional outputs to enable.
encodeConnectedComponentID(int) - Method in class WatershedEncoding
EncodedIntBuffer - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
EncodedIntBuffer(UnsignedIntBuffer, WatershedEncoding) - Constructor for class EncodedIntBuffer
EncodeDirection - Interface in org.anchoranalysis.plugin.image.segment.watershed.encoding
encodeDirection(int, int, int) - Method in interface EncodeDirection
encodeDirection(int, int, int) - Method in class WatershedEncoding
EncodedVoxels - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
EncodedVoxels(Voxels<UnsignedIntBuffer>) - Constructor for class EncodedVoxels
ENCODING - Static variable in class EncodedVoxels
end() - Method in class TextFileOutput
end() - Method in class CheckMark: Called after any calls to CheckMark.check(org.anchoranalysis.mpp.mark.Mark, org.anchoranalysis.mpp.bean.regionmap.RegionMap, org.anchoranalysis.feature.energy.EnergyStack)
end() - Method in class AggregateTriggerBank
end() - Method in class DiscardOutliers
end() - Method in class RelationWithMatches
end() - Method in class GreaterIntersectionWith
end() - Method in class IntensityGreaterEqualThan
end() - Method in class IntersectsWith
end() - Method in class NotTouchingSceneBorder
end() - Method in class ThresholdedFeature
end() - Method in class ObjectFilterPredicate
end() - Method in class ObjectFilterRelation
end() - Method in class AndList
endSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class ConvertImageFormat
endSeries(S, U, InputOutputContext) - Method in class RasterTask: Ends processing of a series.
endSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class MovieFromSlices
ENERGY_STACK - Static variable in class StackIdentifiers: The channels selected as inputs to an optimization routine or for feature calculation.
EnergyMemoList - Class in org.anchoranalysis.mpp.feature.mark: A collection of memoized marks on which energies can be derived.
EnergyMemoList() - Constructor for class EnergyMemoList
EnergyMemoList(EnergySavedInd, EnergyStackWithoutParameters, MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class EnergyMemoList
EnergyMemoList(EnergyMemoList) - Constructor for class EnergyMemoList
EnergyPair - Class in org.anchoranalysis.mpp.feature.energy
EnergyPair(IdentifiablePair, EnergyTotal) - Constructor for class EnergyPair
EnergySavedAll - Class in org.anchoranalysis.mpp.feature.energy.saved
EnergySavedAll() - Constructor for class EnergySavedAll
EnergySavedInd - Class in org.anchoranalysis.mpp.feature.energy.saved
EnergySavedInd() - Constructor for class EnergySavedInd
EnergySavedPairs - Class in org.anchoranalysis.mpp.feature.energy.saved
EnergySavedPairs(AddCriteria<EnergyPair>) - Constructor for class EnergySavedPairs
EnergyScheme - Class in org.anchoranalysis.mpp.feature.energy.scheme: The energy for a feature-list as factorized into different cliques.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair) - Constructor for class EnergyScheme
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair, Optional<DictionaryProvider>, List<NamedBean<Feature<FeatureInputStack>>>) - Constructor for class EnergyScheme
EnergySchemeCreator - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
EnergySchemeCreator() - Constructor for class EnergySchemeCreator
EnergySchemeCreatorByElement - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
EnergySchemeCreatorByElement() - Constructor for class EnergySchemeCreatorByElement
EnergySchemeSet - Class in org.anchoranalysis.mpp.feature.energy.scheme: A set of EnergySchemes each with a name.
EnergySchemeSet(SharedFeatures) - Constructor for class EnergySchemeSet
EnergySchemeWithSharedFeatures - Class in org.anchoranalysis.mpp.feature.energy.scheme
EnergySchemeWithSharedFeatures(EnergyScheme, SharedFeatures, Logger) - Constructor for class EnergySchemeWithSharedFeatures
EnergyStack - Class in org.anchoranalysis.feature.energy: A EnergyStackWithoutParameters with associated parameters in a Dictionary.
EnergyStack(Channel) - Constructor for class EnergyStack: Create from a single Channel.
EnergyStack(EnergyStackWithoutParameters) - Constructor for class EnergyStack: Create from a EnergyStackWithoutParameters without any additional parameters.
EnergyStack(Stack, Dictionary) - Constructor for class EnergyStack: Create from a Stack with associated parameters in a Dictionary.
EnergyStack(Stack) - Constructor for class EnergyStack: Create from a EnergyStack without any additional parameters.
EnergyStack(Dimensions) - Constructor for class EnergyStack: Create a new stack of Dimensions with zero-voxel values, without any additional parameters.
EnergyStack(EnergyStackWithoutParameters, Dictionary) - Constructor for class EnergyStack
energyStack() - Method in class FeatureEvaluator: The specified energy stack.
energyStack() - Static method in class CircleObjectFixture
EnergyStackWithoutParameters - Class in org.anchoranalysis.feature.energy: A stack of channels used as context to calculate features (or calculating energy more broadly).
EnergyStackWithoutParameters(Channel) - Constructor for class EnergyStackWithoutParameters: Create a energy-stack comprised of a single channel
EnergyStackWithoutParameters(Stack) - Constructor for class EnergyStackWithoutParameters: Create a energy-stack comprised of all channels from a stack
EnergyStackWithoutParameters(Dimensions) - Constructor for class EnergyStackWithoutParameters: Create a energy-stack with no channels - but with associated dimensions.
EnergyStackWriter - Class in org.anchoranalysis.mpp.io.output: Writes an energy-stack.
EnergyStackWriter(EnergyStack, Outputter) - Constructor for class EnergyStackWriter
EnergyTotal - Class in org.anchoranalysis.mpp.feature.energy
EnergyTotal(double) - Constructor for class EnergyTotal
EnergyTotal() - Constructor for class EnergyTotal
entryCollection() - Method in class NamedEntries
entrySet() - Method in class MapCreate: The entries in the map.
entrySet() - Method in class FileLabelMap
equalMask(BoundingBox, int) - Method in class Channel: Creates a ObjectMask representing all the voxels in box equal to equalValue.
equals(Object) - Method in class ImageLabelAnnotation
equals(Object) - Method in class CostMatrix
equals(Object) - Method in class Found
equals(Object) - Method in class NotFound
equals(Object) - Method in interface GenerateUniqueParameterization
equals(Object) - Method in class DoubleList
equals(Object) - Method in class DoubleSet
equals(Object) - Method in class IntegerList
equals(Object) - Method in class IntegerSet
equals(Object) - Method in class StringList
equals(Object) - Method in class StringSet
equals(Object) - Method in class RootPath
equals(Object) - Method in class EqualToBean
equals(Object) - Method in class GreaterThanBean
equals(Object) - Method in class GreaterThanEqualToBean
equals(Object) - Method in class LessThanBean
equals(Object) - Method in class LessThanEqualToBean
equals(Object) - Method in class RelationBean
equals(Object) - Method in class RelationToConstant
equals(Object) - Method in class RGBColor
equals(Object) - Method in class TypedEdge
equals(Object) - Method in class Indexable
equals(Object) - Method in class IndexRangeNegative
equals(Object) - Method in class CommonContext
equals(Object) - Method in class TraversalResult
equals(Object) - Method in class FilenameSplitExtension
equals(Object) - Method in class SplitPath
equals(Object) - Method in class TypedValue
equals(Object) - Method in class ParametersUnbound
equals(Object) - Method in class RunningSumParented
equals(Object) - Method in class ChildCacheName
equals(Object) - Method in class ResolvedPart
equals(Object) - Method in class ResolvedPartMap
equals(Object) - Method in class CalculationPart
equals(Object) - Method in class CalculationPartMap
equals(Object) - Method in class FeatureInitialization
equals(Object) - Method in class FeatureInputDimensions
equals(Object) - Method in class FeatureInputEnergy
equals(Object) - Method in class FeatureInputNull
equals(Object) - Method in class FeatureInputResults
equals(Object) - Method in class FeatureCSVMetadata
equals(Object) - Method in class CombinedName
equals(Object) - Method in interface MultiName: If another name is equal to the current name
equals(Object) - Method in class SimpleName
equals(Object) - Method in class LabelledResultsVector
equals(Object...) - Method in class ResultsVector: Does the instance have exactly these values?
equals(Object) - Method in class ResultsVector
equals(Object) - Method in class BoundingBoxesOnPlane
equals(Object) - Method in class SizeXY
equals(Object) - Method in class CalculateLevel
equals(Object) - Method in class CalculateLevelOne
equals(Object) - Method in class BinaryNotOffVoxels
equals(Object) - Method in class BinaryNotOnVoxels
equals(Object) - Method in class BinaryOffVoxels
equals(Object) - Method in class BinaryOnVoxels
equals(Object) - Method in class BinaryVoxelsBase
equals(Dimensions, boolean) - Method in class Dimensions: Checks equality between this object and another Dimensions, but possibly skipping a comparison of image-resolution in the check.
equals(Object) - Method in class Dimensions
equals(Object) - Method in class Resolution
equals(Object) - Method in class Mask
equals(Object) - Method in class OverlappingObject
equals(Object) - Method in class MatchedObject
equals(Object) - Method in class ObjectWithProperties
equals(Object) - Method in class Stack
equals(Object) - Method in class CalculateInputFromPair
equals(Object) - Method in class CalculateNumberVoxels
equals(Object) - Method in class NamedFeatureCalculatorMulti
equals(Object) - Method in class FeatureInputImageMetadata
equals(Object) - Method in class FeatureInputObjectCollection
equals(Object) - Method in class FeatureInputPairObjects
equals(Object) - Method in class FeatureInputSingleObject
equals(Object) - Method in class FeatureInputStack
equals(Object) - Method in class ImageTimestampsAttributes
equals(Object) - Method in class BinaryValuesByte
equals(Object) - Method in class BinaryValuesInt
equals(Object) - Method in class UnsignedBuffer
equals(Object) - Method in class UnsignedBufferAsInt
equals(Object) - Method in class UnsignedByteBuffer
equals(Object) - Method in class UnsignedIntBuffer
equals(Object) - Method in class UnsignedShortBuffer
equals(Object) - Method in class VoxelDataType
equals(Object) - Method in class KernelApplicationParameters
equals(Object) - Method in class ObjectCollection: Checks if two collections are equal in a shallow way.
equals(Object) - Method in class ImageFileEncoding
equals(Object) - Method in class ImageFileShape
equals(Object) - Method in class OptionalNameValue
equals(Object) - Method in class BoundOutputter
equals(Object) - Method in class FileNamerContext
equals(Object) - Method in class NamedFile
equals(Object) - Method in class InputsWithDirectory
equals(Object) - Method in class GlobExtractor.GlobWithDirectory
equals(Object) - Method in class DualPathPredicates
equals(Object) - Method in class PathMatchConstraints
equals(Object) - Method in class FileType
equals(Object) - Method in class ManifestDescription
equals(Object) - Method in class OutputterTarget
equals(Object) - Method in class Outputter
equals(Object) - Method in class NamedPath
equals(Object) - Method in class HelpConfig
equals(Object) - Method in class QuadraticEquationSolver.QuadraticRoots
equals(Object) - Method in class MeanScale
equals(Object) - Method in class EigenvalueAndVector
equals(Object) - Method in class RegionMap
equals(Object) - Method in class RegionMembership
equals(Object) - Method in class RegionMembershipWithFlags
equals(Object) - Method in class CalculateDeriveSingleMemoFromPair
equals(Object) - Method in class FeatureInputMark
equals(Object) - Method in class EnergyPair
equals(Object) - Method in class IndexableMarksWithEnergy
equals(Object) - Method in class FeatureInputAllMemo
equals(Object) - Method in class FeatureInputPairMemo
equals(Object) - Method in class FeatureInputSingleMemo
equals(Object) - Method in class MemoList
equals(Object) - Method in class ColoredMarksWithDisplayStack
equals(Object) - Method in class MarksWithDisplayStack
equals(Object) - Method in class OverlayMark
equals(Object) - Method in class IdentifiablePair
equals(Object) - Method in class PairPxlMarkMemo
equals(Object) - Method in class ProposerContext
equals(Object) - Method in class DualStack
equals(Object) - Method in class FeedbackBeginParameters
equals(Object) - Method in class FeedbackEndParameters
equals(Object) - Method in class KernelWithIdentifier
equals(Object) - Method in class IndexableOverlays
equals(Object) - Method in class OverlayObjectMask
equals(Object) - Method in class Overlay
equals(Object) - Method in class ObjectDrawAttributes
equals(Object) - Method in class AxisLimits
equals(Object) - Method in class ObjectsToCompare
equals(Object) - Method in class CalculateLevelListBase
equals(Object) - Method in class CalculateLevelRelativeToThreshold
equals(Object) - Method in class ClampHistogramMax
equals(Object) - Method in class Constant
equals(Object) - Method in class EmptyHistogramConstant
equals(Object) - Method in class IfGreaterThan
equals(Object) - Method in class IfLessThan
equals(Object) - Method in class Maximum
equals(Object) - Method in class Minimum
equals(Object) - Method in class Otsu
equals(Object) - Method in class OtsuWeighted
equals(Object) - Method in class Quantile
equals(Object) - Method in class MorphologicalIterations
equals(Object) - Method in class CalculateIntersecting
equals(Object) - Method in class CalculateDeriveObjectInput
equals(Object) - Method in class CalculateInputFromDelegate
equals(Object) - Method in class CalculateInputFromDelegateOption
equals(Object) - Method in class CalculateIncrementalOperationMap
equals(Object) - Method in class CalculateObjectMask
equals(Object) - Method in class CalculateShellObjectMask
equals(Object) - Method in class CalculateDilation
equals(Object) - Method in class CalculateDilationMap
equals(Object) - Method in class CalculateErosion
equals(Object) - Method in class CalculateErosionMap
equals(Object) - Method in class CalculateHistogram
equals(Object) - Method in class CalculateHistogramMasked
equals(Object) - Method in class ChangeableOutputSequence
equals(Object) - Method in class FeatureExporterContext
equals(Object) - Method in class InitializationWithEnergyStack
equals(Object) - Method in class LabelledResultsVectorWithThumbnail
equals(Object) - Method in class ResultsVectorWithThumbnail
equals(Object) - Method in class NamedChannel
equals(Object) - Method in class ImageCSVLabellerInitialization
equals(Object) - Method in class ImageLabellerStringMapInitialization
equals(Object) - Method in class CopyContext
equals(Object) - Method in class FileDetails
equals(Object) - Method in class SortedSetChannel
equals(Object) - Method in class SortedSetSlice
equals(Object) - Method in class AnonymizeSharedState
equals(Object) - Method in class AllSlicesMaskEverythingNonZero
equals(Object) - Method in class AllSlicesMaskNonZero
equals(Object) - Method in class CenterSlice
equals(Object) - Method in class CenterSliceBase
equals(Object) - Method in class CenterSliceWindow
equals(Object) - Method in class GreatestAreaSlice
equals(Object) - Method in class IndexedRegionBase
equals(Object) - Method in class SelectSlicesBase
equals(Object) - Method in class SelectSlicesWithIndexBase
equals(Object) - Method in class Specific
equals(Object) - Method in class DistanceIndex
equals(Object) - Method in class DistanceIndexTwice
equals(Object) - Method in class ConvertedInput
equals(Object) - Method in class CalculateDeriveMarkCollectionInput
equals(Object) - Method in class CalculateDeriveMarkInput
equals(Object) - Method in class CalculateOverlap
equals(Object) - Method in class CalculateOverlapMask
equals(Object) - Method in class CalculateOverlapMIP
equals(Object) - Method in class CalculateOverlapMIPBase
equals(Object) - Method in class CalculateOverlapMIPRatio
equals(Object) - Method in class KernelDeath.MarkAnd
equals(Object) - Method in class ToVoxelized
equals(Object) - Method in class HOGParameters
equals(Object) - Method in class FitResult
equals(Object) - Method in class CalculateEllipseLeastSquares
equals(Object) - Method in class ObjectWithEllipse
equals(Object) - Method in class CalculateEllipsoidLeastSquares
equals(Object) - Method in class BoundingBox
equals(Object) - Method in class Extent
equals(Object) - Method in class Orientation
equals(Object) - Method in class Orientation2D
equals(Object) - Method in class Orientation3DEulerAngles
equals(Object) - Method in class OrientationAxisAngle
equals(Object) - Method in class OrientationRotationMatrix
equals(Object) - Method in class Point2d
equals(Object) - Method in class Point2f
equals(Object) - Method in class Point2i
equals(Object) - Method in class Point3d
equals(Object) - Method in class Point3f
equals(Object) - Method in class Point3i
equals(Object) - Method in class Tuple3d
equals(Object) - Method in class Tuple3f
equals(Object) - Method in class Tuple3i
equals(Object) - Method in class Vector3d
equals(Object) - Method in class ScaleFactor
equalsDeep(Channel, boolean) - Method in class Channel: Are the two channels equal using a deep voxel by voxel comparison?
equalsDeep(Stack, boolean) - Method in class Stack: Are the two stack equal using a deep voxel by voxel comparison of each channel?
equalsDeep(BoundedVoxels<?>) - Method in class BoundedVoxels: Performs a deep equality check, that includes checking that each voxel has an identical value.
equalsDeep(ObjectCollection) - Method in class ObjectCollection: Checks if two collections are equal in a deeper way.
equalsDeep(ObjectMask) - Method in class ObjectMask: A deep equality check with another ObjectMask.
equalsDeep(Voxels<?>) - Method in class Voxels: Are the voxels identical to another voxels (deep equals)?
equalsDeep(Mark) - Method in class Ellipse
equalsDeep(Mark) - Method in class Ellipsoid
equalsDeep(Mark) - Method in class MarkWithPositionAndSingleRadius
equalsDeep(Mark) - Method in class Mark
equalsDeep(MarkCollection) - Method in class MarkCollection
equalsDeep(Mark) - Method in class MarkWithPosition
equalsDeep(Mark) - Method in class PointListBase
equalsID(Object) - Method in class Mark
equalsIgnoreZ(Extent) - Method in class Extent: Checks for equality with another extent ignoring any differences in the Z dimension.
equalsPrecision(double, Object...) - Method in class ResultsVector: Like ResultsVector.equals(Object) but includes a tolerance for checking equality of the doubles.
equalsTolerance(Point3d, double) - Method in class Point3d: Checks if this point is equal to another Point3d accepting a tolerance between double values.
EqualTo - Class in org.anchoranalysis.math.relation: Returns true if two values are equal, and false otherwise.
EqualTo() - Constructor for class EqualTo
EqualToBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 == double2.
EqualToBean() - Constructor for class EqualToBean
equalToPrimitive(Voxels<UnsignedByteBuffer>, byte, ScalarThreeDimensionalConsumer) - Static method in class IterateVoxelsEqualTo: Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
equalToPrimitiveSlice(Voxels<UnsignedByteBuffer>, int, byte, ScalarThreeDimensionalConsumer) - Static method in class IterateVoxelsEqualTo: Like IterateVoxelsEqualTo.equalToPrimitive(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>, byte, org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer) but only iterates over one specific z-slice.
equalToReusePoint(Voxels<UnsignedByteBuffer>, byte, Consumer<Point3i>) - Static method in class IterateVoxelsEqualTo: Iterates all points with a specific voxel intensity-value, reusing the Point3i in each iteration.
erode(ObjectMask, int, boolean) - Static method in class MorphologicalErosion: Performs a morphological erosion on an ObjectMask.
erode(ObjectMask, int, boolean, Optional<AcceptIterationPredicate>) - Static method in class MorphologicalErosion: Performs a morphological erosion on an ObjectMask - with a postcondition.
erode(BinaryVoxels<UnsignedByteBuffer>, int, boolean, Optional<Predicate<Point3i>>) - Static method in class MorphologicalErosion: Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.
Erode - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs an erosion morphological operation on BinaryVoxels.
Erode() - Constructor for class Erode
Erode - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Erode() - Constructor for class Erode
Erode - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
Erode() - Constructor for class Erode
ErosionKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological: Erosion with a 3x3 or 3x3x3 kernel size.
ErosionKernel() - Constructor for class ErosionKernel: Default constructor.
errorMessageIfTooFewPixels() - Method in class ImageMomentsBase
errorMessageIfTooFewPixels() - Method in class PrincipalAxisEccentricity
errorMessageIfTooFewPixels() - Method in class PrincipalAxisLength
errorMessageIfTooFewPixels() - Method in class PrincipalAxisOrientation
errorMessageIfTooFewPixels() - Method in class RatioPrincipalAxisLength
ErrorNode - Class in org.anchoranalysis.mpp.proposer.error
ErrorNode() - Constructor for class ErrorNode
ErrorNodeException - Exception in org.anchoranalysis.mpp.proposer.error
ErrorNodeException(String) - Constructor for exception ErrorNodeException
ErrorNodeException(Exception) - Constructor for exception ErrorNodeException
ErrorNodeImpl - Class in org.anchoranalysis.mpp.proposer.error
ErrorNodeNull - Class in org.anchoranalysis.mpp.proposer.error: Singleton that does nothing with errors
ErrorReporter - Interface in org.anchoranalysis.core.log.error: Reports errors as they occur.
errorReporter() - Method in class Logger: Where errors are reported to.
ErrorReporterBase - Class in org.anchoranalysis.core.log.error: Utility base class for common error-reporting formatting.
ErrorReporterBase(Consumer<String>) - Constructor for class ErrorReporterBase
ErrorReporterForTask - Class in org.anchoranalysis.experiment.task: An error-reporter that replaces particular errors/exceptions with user-friendly messages.
ErrorReporterForTask(MessageLogger) - Constructor for class ErrorReporterForTask
ErrorReporterIntoLog - Class in org.anchoranalysis.core.log.error: Records errors, by writing them into a logger.
ErrorReporterIntoLog(MessageLogger) - Constructor for class ErrorReporterIntoLog: Create for a message-logger.
ErrorReporterIntoString - Class in org.anchoranalysis.core.log.error: Logs error messages into a String via StringBuilder.
ErrorReporterIntoString(StringBuilder) - Constructor for class ErrorReporterIntoString: Creates for a particular StringBuilder.
EXCEPTED_DOUBLE_EXTENSIONS - Static variable in class ExtensionUtilities: Particular extensions with a double period, that are exceptionally checked for, and treated as a single extension.
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
exchange(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStack) - Method in class MarksWithEnergyBreakdown
exchange(int, VoxelizedMarkMemo) - Method in class MarksWithEnergyBreakdown
exchange(int, VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
exchange(int, VoxelizedMarkMemo, EnergyStack) - Method in class VoxelizedMarksWithEnergy
exchange(int, EnergyTotal) - Method in class EnergySavedInd
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class EnergySavedPairs
exchange(EnergySavedInd, int, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class EnergyMemoList
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class UpdatableMarksList
exchange(int, Mark) - Method in class MarkCollection
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in interface UpdatableMarks
exchangeOnUpdatablePairList(UpdatableMarksList, Mark, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
Exclude<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Excludes all inputs whose identifiers match a regular expression.
Exclude() - Constructor for class Exclude
execExperiment(String, String) - Static method in class UnitTestCompareUtilities: As we use a common format for storing our tests for the different modules.
execExperimentInTemporary(String, String, boolean, Path) - Static method in class UnitTestCompareUtilities: As we use a common format for storing our tests for the different modules.
execute(Outputter, List<T>, ParametersExperiment) - Method in class DebugDependentProcessor
execute(Outputter, List<T>, ParametersExperiment) - Method in class JobProcessor: The job processor is expected to remove items from the inputs-list as they are consumed so as to allow garbage-collection of these items before all jobs are processed (as the list might be quite large).
execute(Outputter, List<T>, ParametersExperiment) - Method in class ParallelProcessor
execute(Outputter, List<T>, ParametersExperiment) - Method in class SequentialProcessor
execute(T) - Method in class CalculationPart: This performs the actual calculation when needed.
execute(T, U) - Method in class CalculationPartMap: Calculates a result for a particular input and key.
execute(FeatureInputPairObjects) - Method in class CalculateInputFromPair
execute(FeatureInputSingleObject) - Method in class CalculateNumberVoxels
execute() - Method in interface WriterExecuteBeforeEveryOperation: Is called before every operation
execute() - Method in class HungarianAlgorithm: Execute the algorithm.
execute(FeatureInputPairMemo) - Method in class CalculateDeriveSingleMemoFromPair
execute(FeatureInputStack) - Method in class CalculateDeriveObjectInput
execute(T) - Method in class CalculateInputFromDelegate
execute(FeatureInputSingleObject, Integer) - Method in class CalculateIncrementalOperationMap
execute(FeatureInputSingleObject) - Method in class CalculateObjectMask
execute(FeatureInputSingleObject) - Method in class CalculateShellObjectMask
execute(FeatureInputStack) - Method in class CalculateHistogram
execute(FeatureInputStack) - Method in class CalculateHistogramMasked
execute(FeatureInputAllMemo) - Method in class CalculateDeriveMarkCollectionInput
execute(FeatureInputAllMemo) - Method in class CalculateDeriveMarkInput
execute(FeatureInputPairMemo) - Method in class CalculateOverlap
execute(FeatureInputPairMemo) - Method in class CalculateOverlapMask
execute(FeatureInputPairMemo) - Method in class CalculateOverlapMIPBase
execute(FeatureInputSingleObject) - Method in class CalculateEllipseLeastSquares
execute(FeatureInputSingleObject) - Method in class CalculateEllipsoidLeastSquares
executeAndAssertCount(int, int, CheckedRunnable<OperationFailedException>) - Static method in class MockFeatureWithCalculationFixture: Executes an operation, and afterwards asserts an expected number of times certain internal methods are called on a mock-calculation.
executeEachWithMonitor(String, List<T>) - Method in class MonitoredSequentialExecutor: Executes code for each element of inputs in serial, providing log-reports as to how many are finished, remain etc.
executeExperiment(ExecutionArguments) - Method in class Experiment: Executes the experiment.
executeExperiment(ExecutionArguments) - Method in class OutputExperiment: Executes the experiment for given arguments.
executeExperiment(ExecutionArguments, boolean, MessageLogger) - Method in class ExperimentExecutor: Executes an experiment after finding a single experiment XML file, and reading the experiment from this file.
executeExperiment(ExecutionArguments) - Method in class QuickExperiment
executeExperiment(ExecutionArguments) - Method in class QuickMultiDatasetExperiment
executeExperiment(ExecutionArguments) - Method in class QuickMultiDatasetStructuredExperiment
executeExperimentWithParameters(ParametersExperiment) - Method in class InputOutputExperiment
executeExperimentWithParameters(ParametersExperiment) - Method in class OutputExperiment: Executes the experiment for parameters.
executeJob(ParametersUnbound<T, S>) - Method in class Task: Runs the task on one particular input (a job).
executeLogStats(Outputter, List<T>, ParametersExperiment) - Method in class JobProcessor: Executes the tasks, gathers statistics, and logs them
executePhase() - Method in class HungarianAlgorithm: Execute a single phase of the algorithm.
executingTasks() - Method in class ConcurrentJobMonitor
ExecutionArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's execution (in its entirety) in addition to its bean specification.
ExecutionArguments(Path) - Constructor for class ExecutionArguments
ExecutionArguments() - Constructor for class ExecutionArguments
ExecutionTimeRecorder - Class in org.anchoranalysis.core.time: Records the execution-time of particular operations.
ExecutionTimeRecorder() - Constructor for class ExecutionTimeRecorder
executionTimeRecorder() - Method in class ParametersExperiment: Allows execution-times to be recorded for particular operations.
ExecutionTimeRecorderFactory - Class in org.anchoranalysis.experiment.time: Creates an instance of ExecutionTimeRecorder depending in what outputs are enabled.
ExecutionTimeRecorderIgnore - Class in org.anchoranalysis.core.time: An implementation of ExecutionTimeRecorder that is a simple placeholder that does nothing.
ExecutionTimeRecorderIgnore() - Constructor for class ExecutionTimeRecorderIgnore
executionTimeStatistics() - Method in class ParametersExperiment
executionTimeTotal() - Method in class TaskStatistics: Execution-time of all jobs in milliseconds, ignoring any parallelism.
exists() - Method in interface Finder
exists() - Method in class FinderExperimentFileDirectories
exists() - Method in class FinderSingleDirectory
exists() - Method in class FinderSingleFile
existsWith(BoundingBox) - Method in class BoundingBoxIntersection: Does intersection exist with another bounding-box?
existsWithAny(List<BoundingBox>) - Method in class BoundingBoxIntersection: Does intersection exist with with any of the others in the list?
expectedOutputs() - Method in class DecodeMaskRCNN
expectedOutputs() - Method in class DecodeEAST
Experiment - Class in org.anchoranalysis.experiment.bean
Experiment() - Constructor for class Experiment
ExperimentExecutionException - Exception in org.anchoranalysis.experiment: An exception that occurs when an experiment is executed.
ExperimentExecutionException(String) - Constructor for exception ExperimentExecutionException
ExperimentExecutionException(Throwable) - Constructor for exception ExperimentExecutionException
ExperimentExecutionException(String, Throwable) - Constructor for exception ExperimentExecutionException: A string message displayed to the user as well as a stack-trace of the cause
ExperimentExecutor - Class in org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
ExperimentExecutorFactory - Class in org.anchoranalysis.launcher.executor: Creates an ExperimentExecutor.
ExperimentFactory - Class in org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParam<Path> factory for experiments.
ExperimentFeedbackContext - Class in org.anchoranalysis.experiment.task: Objects to give the user feedback about different aspects of the experiment.
ExperimentFeedbackContext(StatefulMessageLogger, boolean, ExecutionTimeRecorder) - Constructor for class ExperimentFeedbackContext
ExperimentIdentifier - Class in org.anchoranalysis.experiment.bean.identifier
ExperimentIdentifier() - Constructor for class ExperimentIdentifier
ExperimentIdentifierAuto - Class in org.anchoranalysis.experiment.bean.identifier: Automatically populates a experiment-name and version number
ExperimentIdentifierAuto() - Constructor for class ExperimentIdentifierAuto
ExperimentIdentifierConstant - Class in org.anchoranalysis.experiment.bean.identifier: Defines constants for name and version of an experiment
ExperimentIdentifierConstant() - Constructor for class ExperimentIdentifierConstant
ExperimentIdentifierConstant(String, String) - Constructor for class ExperimentIdentifierConstant
experimentIdentifierForOutputPath() - Method in class ParametersExperiment: The experiment-identifier to use in the output-path, if one should be used.
ExperimentLauncherFromShell - Class in org.anchoranalysis.test.experiment.launcher: Launches an experiment by calling the application 'anchor' via the shell.
ExperimentLauncherFromShell(TestLoader) - Constructor for class ExperimentLauncherFromShell
ExperimentResultsExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure: Finds some files produced in a previous experiment assuming a certain structure
ExperimentResultsExperimentStructure() - Constructor for class ExperimentResultsExperimentStructure
experimentSelectParam(CommandLine, Path) - Static method in class SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an experiment nothing, then default experiment is used
ExperimentState - Interface in org.anchoranalysis.mpp.segment.bean
ExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure: A PathPrefixer that combines a prefix with an experimentType.
ExperimentStructure() - Constructor for class ExperimentStructure
ExportFeatures<T extends InputFromManager,S,U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature: Calculates features and exports them as a CSV file.
ExportFeatures() - Constructor for class ExportFeatures
ExportFeaturesStyle - Class in org.anchoranalysis.plugin.image.task.bean.feature: Visual style for how features are exported.
ExportFeaturesStyle() - Constructor for class ExportFeaturesStyle
ExportFeaturesStyle(boolean, boolean, boolean) - Constructor for class ExportFeaturesStyle
ExportImageHistograms - Class in org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Exports a histogram of voxel intensities as a CSV file for each channel of an image.
ExportImageHistograms() - Constructor for class ExportImageHistograms
ExportObjectsAsCroppedImages - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects: Exports a cropped image for each object-mask showing its context within an image
ExportObjectsAsCroppedImages() - Constructor for class ExportObjectsAsCroppedImages
ExportObjectsBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
ExportObjectsBase() - Constructor for class ExportObjectsBase
ExportObjectsFromCSV - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects: Given a CSV with a point representing one or more object-masks, these object-masks are extracted from a segmentation.
ExportObjectsFromCSV() - Constructor for class ExportObjectsFromCSV
ExportReportFeatures<T extends InputFromManager,S,U> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task: A base class for tasks that calculate and export ReportFeatures.
ExportReportFeatures() - Constructor for class ExportReportFeatures
ExportReportFeaturesFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task: Creates a report of feature values from a DeserializedManifest and a ManifestCouplingDefinition.
ExportReportFeaturesFromManifest() - Constructor for class ExportReportFeaturesFromManifest
ExportReportFeaturesFromMulti - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task: Creates a report of feature values from a DefineOutputter and a MultiInput.
ExportReportFeaturesFromMulti() - Constructor for class ExportReportFeaturesFromMulti
ExportSharedObjects - Interface in org.anchoranalysis.mpp.io.input: A method that copies certain shared-objects.
ExtendInZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
ExtendInZ() - Constructor for class ExtendInZ
ExtendInZWithinContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Extends an object (2D/3D) as much as it can within the z-slices of a containing object
ExtendInZWithinContainer() - Constructor for class ExtendInZWithinContainer
extendWith(int) - Method in class InterpolatorImgLib2: Switches to extend constant-value out-of-bounds strategy
extension() - Method in class ImageFileAttributes: The file extension of the file-path.
extensionAsArray() - Method in enum NonImageFileFormat: The extension (without a period) as an array.
ExtensionCount - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Remembers each unique extension, and associated count
ExtensionCount() - Constructor for class ExtensionCount
extensionSuffix(OutputWriteSettings) - Method in class ObjectOutputStreamGenerator
extensionSuffix(OutputWriteSettings) - Method in class SerializedGenerator: Appended to the standard "serialized" extension, to form the complete extension
extensionSuffix(OutputWriteSettings) - Method in class XStreamGenerator
ExtensionUtilities - Class in org.anchoranalysis.core.system.path: Extracting a file-extension from a path according to rules.
extensionWithoutPeriod() - Method in enum NonImageFileFormat: The extension without any leading period.
extensionWithPeriod() - Method in enum NonImageFileFormat: The extension with a leading period.
extent() - Method in class EnergyStack: The width and height and depth of all Channels in the stack.
extent() - Method in class EnergyStackWithoutParameters: The width and height and depth of all Channels in the stack.
extent() - Method in class BoundingBoxesOnPlane
extent() - Method in class Channel: The size of the voxels across three dimensions.
extent() - Method in class Dimensions: The width and height and depth of the image.
extent(Extent) - Method in enum OrientationChange: A Extent that describes extent after the orientation change.
extent() - Method in class Mask: The size of the voxels across three dimensions.
extent() - Method in class DisplayStack: The width and height and depth of all channels in the Stack.
extent() - Method in class RGBStack: The width and height and depth of the image.
extent() - Method in class Stack: The width and height and depth of the image.
extent() - Method in class BinaryVoxels: The size of the voxels across three dimensions.
extent() - Method in class BoundedVoxels: The size of the voxels across three dimensions, and also the size of the associated bounding-box.
extent() - Method in class FromByte
extent() - Method in class FromFloat
extent() - Method in class FromInt
extent() - Method in class FromShort
extent() - Method in interface SliceBufferIndex: The size of each buffer.
extent() - Method in class SlidingBuffer: The size of the voxels across three dimensions.
extent() - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The size of the associated SlidingBuffer.
extent() - Method in class ObjectMask: The size of the object-mask's bounding-box across three dimensions.
extent() - Method in class Voxels: The size of the voxels across three dimensions.
extent() - Method in class VoxelsUntyped: The size of the voxels across three dimensions.
extent - Variable in class ConvertTo: The size of the source and destination buffers.
Extent<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Width/height/depth of energy-stack in pixels depending on axis.
Extent() - Constructor for class Extent
extent() - Method in class EncodedVoxels
extent() - Method in class BoundingBox: Dimensions in pixels needed to represent the bounding box.
Extent - Class in org.anchoranalysis.spatial.box: The sizes: width, height, depth etc.
Extent(int, int) - Constructor for class Extent: Creates with with only X and Y dimensions.
Extent(int, int, int) - Constructor for class Extent: Creates with X and Y and Z dimensions.
EXTENT_X - Static variable in class HDF5PathHelper: Attribute for x dimension of extent
EXTENT_Y - Static variable in class HDF5PathHelper: Attribute for y dimension of extent
EXTENT_Z - Static variable in class HDF5PathHelper: Attribute for z dimension of extent
extentAfterAnyScaling() - Method in class ScaleableBackground
ExtentMatchHelper - Class in org.anchoranalysis.image.voxel: Checks if the Extents of two BoundingBoxes are identical.
ExteriorContour - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Finds the exterior outer contour for a Mask that forms its outline.
ExteriorContour() - Constructor for class ExteriorContour
extract(List<T>) - Method in class IndexRangeNegative: Extracts a subset of elements from a list according to the specified index/range.
extract() - Method in class Channel: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class BinaryVoxels: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class BoundedVoxels: Extracts value from voxels using global coordinates (relative to the image as a whole).
extract() - Method in class ObjectMask: Provides methods to read/copy/duplicate regions of voxels.
extract() - Method in class Voxels: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class VoxelsFloat
extract() - Method in class VoxelsUnsignedByte
extract() - Method in class VoxelsUnsignedInt
extract() - Method in class VoxelsUnsignedShort
extract() - Method in class VoxelsUntyped: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract(String) - Static method in class GlobExtractor: Extracts a glob, and a directory portion if it exists from a string with a wildcard.
extractAsDouble(Dictionary, String) - Static method in class FromDictionaryBase
ExtractBoundingBoxAreaFromStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box: An iterable-generator that outputs the portion of a stack corresponding to a bounding-box
ExtractBoundingBoxAreaFromStackGenerator(ScaleableBackground) - Constructor for class ExtractBoundingBoxAreaFromStackGenerator
ExtractCenterSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts the slice at the center (rounding down) of the range of z-stacks.
ExtractCenterSlice() - Constructor for class ExtractCenterSlice
extractChannel(String, boolean) - Method in class ChannelSource
extractChannel(String, boolean, int) - Method in class ChannelSource
extractChannel(Stack, boolean, int) - Method in class ChannelSource
extractChannelForBoundingBox(int, BoundingBox) - Method in class DisplayStack: Creates a new Channel that refers to only a BoundingBox portion of the DisplayStack.
ExtractDerivedParameter<S,T> - Class in org.anchoranalysis.bean.initializable.property: Extracts one type of parameter from another, if possible.
ExtractDerivedParameter(Class<?>, Function<S, T>) - Constructor for class ExtractDerivedParameter: Creates with only a targetClass.
ExtractDerivedParameter(Class<?>, Function<S, T>, Class<?>) - Constructor for class ExtractDerivedParameter: Creates with a classOfTarget and a baseClassOfSource.
extractExtension(String) - Static method in class ExtensionUtilities: Extracts the extension from a filename.
extractExtension(Path) - Static method in class ExtensionUtilities: Like ExtensionUtilities.extractExtension(String) but accepts a Path instead of a String.
extractFrom(T) - Method in class ExtractIdentifier
extractFrom(T) - Method in class ExtractIdentifierAndPath
extractFrom(T) - Method in class ExtractPath
extractFrom(T) - Method in class SummarizerInputFromManager
extractFromVoxelized(VoxelizedMark) - Method in class AllSlicesMaskEverythingNonZero
extractFromVoxelized(VoxelizedMark) - Method in class AllSlicesMaskNonZero
extractFromVoxelized(VoxelizedMark) - Method in class SelectSlicesWithIndexBase
ExtractIdentifier<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts the identifier from an InputFromManager to summarize further.
ExtractIdentifier() - Constructor for class ExtractIdentifier
ExtractIdentifierAndPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts the identifier and path from an InputFromManager to summarize further.
ExtractIdentifierAndPath() - Constructor for class ExtractIdentifierAndPath
extractIfPossible(S) - Method in class ExtractDerivedParameter: Extracts a derived parameter if possible from parameter.
extractKey(ImageMetadataInput) - Method in class BitDepth
extractKey(ImageMetadataInput) - Method in class NumberChannels
extractKey(ImageMetadataInput) - Method in class SummarizerImageMetadataSimple
extractObjectForSummary(T) - Method in class SummarizeBase: Extract object for summary.
extractObjectForSummary(T) - Method in class SummarizeInputs
ExtractPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts a Path from an input to summarize further.
ExtractPath() - Constructor for class ExtractPath
extractRegionFromStack(BoundingBox) - Method in class ScaleableBackground: Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box
extractScaledValue(byte[], int, boolean) - Method in class ToUnsignedByteWithScaling: Extracts a value from the source-array, and apply any scaling and clamping.
extractScaledValue(byte[], int, boolean) - Method in class UnsignedByteFromUnsignedByteNoInterleavingScale
extractScaledValue(byte[], int, boolean) - Method in class UnsignedByteFromUnsignedInt
extractScaledValue(byte[], int, boolean) - Method in class UnsignedByteFromUnsignedShort
extractScore(T) - Method in class ExtractScoreSize
extractScore(DualVoxelizedMarks) - Method in class FromDualVoxelizedMarks
extractScore(VoxelizedMarksWithEnergy) - Method in class FromVoxelizedMarksWithEnergy
extractScore(ToVoxelized<T>) - Method in class ToPixelizedExtracter
ExtractScoreSize<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
ExtractScoreSize() - Constructor for class ExtractScoreSize
extractScoreSizeReport() - Method in class AssignMode
extractScoreSizeReport() - Method in class DirectAssignMode
extractScoreSizeReport() - Method in class TransformationAssignMode
extractScoreSizeState() - Method in class AssignMode
extractScoreSizeState() - Method in class DirectAssignMode
extractScoreSizeState() - Method in class TransformationAssignMode
extractSize(T) - Method in class ExtractScoreSize
extractSize(DualVoxelizedMarks) - Method in class FromDualVoxelizedMarks
extractSize(VoxelizedMarksWithEnergy) - Method in class FromVoxelizedMarksWithEnergy
extractSize(ToVoxelized<T>) - Method in class ToPixelizedExtracter
extractSlice(int) - Method in class EnergyStack: Extract a particular z-slice from the EnergyStack as a new stack.
extractSlice(int) - Method in class EnergyStackWithoutParameters: Extract a particular z-slice from the EnergyStackWithoutParameters as a new stack.
extractSlice(int) - Method in class Channel: Creates a new Channel containing only one particular slice.
extractSlice(int) - Method in class Mask: Creates a new Mask containing only one particular slice.
extractSlice(int) - Method in class DisplayStack: Extract a particular z-slice from the DisplayStack as a new stack, applying any applicable conversion.
extractSlice(int) - Method in class RGBStack: Extract a particular z-slice from the Stack as a new stack.
extractSlice(int) - Method in class Stack: Extract a particular z-slice from the Stack as a new stack.
extractSlice(int) - Method in class StackNotUniformSized: Creates a new StackNotUniformSized containing only one particular slice for each respective channel.
extractSlice(int) - Method in class BoundedVoxels: Extracts a particular slice.
extractSlice(int, boolean) - Method in class ObjectMask: Extracts one particular slice as an object-mask
ExtractSlice - Class in org.anchoranalysis.plugin.image.task.bean.slice: Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
ExtractSlice() - Constructor for class ExtractSlice
ExtractSliceRange - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive).
ExtractSliceRange() - Constructor for class ExtractSliceRange
extractStack(ProvidesStackInput, StackProvider, InputOutputContext) - Static method in class FeatureCalculatorRepeated
extractTupleForBoundingBox(BoundingBox) - Method in class BoundingBoxAlongAxisBase
extractTupleForBoundingBox(BoundingBox) - Method in class BoundingBoxExtentAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class BoundingBoxMaximumAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class BoundingBoxMinimumAlongAxis
extractUpToThreeChannels() - Method in class Stack: Extracts the first three Channels as a new Stack.
ExtractWeightFromMark - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
ExtractWeightFromMark() - Constructor for class ExtractWeightFromMark

F

factory() - Method in class Voxels: A factory for creating voxels with a particular buffer-type.
FailureOnlyMessageLogger - Class in org.anchoranalysis.experiment.log: Writes text to a file, but only if FailureOnlyMessageLogger.close(boolean, boolean) is called with successful==true.
FailureOnlyMessageLogger(String, OutputterChecked, ErrorReporter, boolean) - Constructor for class FailureOnlyMessageLogger
Feature<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean: Base class for a measurement that calculates a result (double) given input parameters.
Feature() - Constructor for class Feature: Creates with the default initializer.
Feature(BeanInitializer<FeatureInitialization>) - Constructor for class Feature: Creates with a custom initializer.
feature() - Method in class MarksInitialization
FeatureAllMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
FeatureAllMemo() - Constructor for class FeatureAllMemo
FeatureAsIndividualProportionate - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair: Calculates each feature individually, and combines them using the ratios between itemProportionate as weights
FeatureAsIndividualProportionate() - Constructor for class FeatureAsIndividualProportionate
FeatureBinary<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A base class for a Feature that is a binary-function of the results from two other features.
FeatureBinary() - Constructor for class FeatureBinary
FeatureCalculationCache<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: A context in which to calculate features while caching certain duplicated internal calculations among the features.
FeatureCalculationContext<S> - Class in org.anchoranalysis.plugin.image.task.feature: The context in which features are calculated, so as to be later exported as a CSV.
FeatureCalculationContext(FeatureResultsAndThumbnails, S, FeatureNameList, Optional<String>, ExecutionTimeRecorder, boolean, InputOutputContext) - Constructor for class FeatureCalculationContext: Default constructor.
FeatureCalculationException - Exception in org.anchoranalysis.feature.calculate: When the calculation of a feature cannot complete successfully.
FeatureCalculationException(String) - Constructor for exception FeatureCalculationException: Creates with a message only.
FeatureCalculationException(Throwable) - Constructor for exception FeatureCalculationException: Creates with a cause only.
FeatureCalculationException(String, Throwable) - Constructor for exception FeatureCalculationException: Creates with both a message and a cause.
FeatureCalculationInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate: Gives a FeatureInput the necessary context for feature-calculation, including associating it with a cache.
FeatureCalculationResults - Interface in org.anchoranalysis.feature.io.results.calculation: Stores LabelledResultsVector as they are calculated, and writes to the file-system.
FeatureCalculationResultsFactory - Class in org.anchoranalysis.feature.io.results.calculation: Creates FeatureCalculationResults.
FeatureCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate: Calculates FeatureCalculationInput when passed a particular Feature and corresponding FeatureCalculationInput.
FeatureCalculatorCache - Class in org.anchoranalysis.feature.session.calculator: Adds a cache to a FeatureCalculatorSingle or FeatureCalculatorMulti.
FeatureCalculatorFromProvider<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates feature or feature values.
FeatureCalculatorFromProvider(ProvidesStackInput, Optional<StackProvider>, InputOutputContext) - Constructor for class FeatureCalculatorFromProvider
FeatureCalculatorMulti<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.bound: Like a FeatureCalculator but is permanently associated with one or more Features.
FeatureCalculatorMultiChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.bound: A FeatureCalculatorMulti but changes the input before calculation.
FeatureCalculatorMultiChangeInput(FeatureCalculatorMulti<T>, Consumer<T>) - Constructor for class FeatureCalculatorMultiChangeInput
FeatureCalculatorRepeated - Class in org.anchoranalysis.plugin.image.task.feature.calculator
FeatureCalculatorSingle<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.bound: Like a FeatureCalculator but is permanently associated with a single Feature.
FeatureCalculatorSingleChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.bound: A FeatureCalculatorSingle but changes the input before calculation.
FeatureCalculatorSingleChangeInput(FeatureCalculatorSingle<T>, Consumer<T>) - Constructor for class FeatureCalculatorSingleChangeInput
FeatureCalculatorSingleFromMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.bound: Exposes a FeatureCalculatorMulti as a FeatureCalculatorSingle.
FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T>) - Constructor for class FeatureCalculatorSingleFromMulti: Creates from a FeatureCalculatorMulti.
FeatureConvertUnits<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
FeatureConvertUnits(Feature<T>, SpatialUnits.UnitSuffix) - Constructor for class FeatureConvertUnits
FeatureConvertUnits() - Constructor for class FeatureConvertUnits
FeatureCostAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Assigns an objects from one set of objects to another based upon a cost (degree of overlap).
FeatureCostAssigner() - Constructor for class FeatureCostAssigner
FeatureCSVMetadata - Class in org.anchoranalysis.feature.io.csv: What's needed to output a CSV other than the actual data items.
FeatureCSVMetadata(String, List<String>) - Constructor for class FeatureCSVMetadata
FeatureCSVWriter - Class in org.anchoranalysis.feature.io.csv: Writes the results of feature-calculations as a CSV file.
FeatureCSVWriter(CSVWriter, boolean) - Constructor for class FeatureCSVWriter: Creates for a CSVWriter.
FeatureCSVWriterCreator - Interface in org.anchoranalysis.feature.io.results.calculation: To facilitate delayed creation of a FeatureCSVWriter.
FeatureDeriveFromPair - Class in org.anchoranalysis.image.feature.bean.object.pair: Base class for evaluating FeaturePairObjects in terms of another feature that operations on elements (first, second, merged etc.)
FeatureDeriveFromPair() - Constructor for class FeatureDeriveFromPair
FeatureDeriveFromPair(Feature<FeatureInputSingleObject>) - Constructor for class FeatureDeriveFromPair
featureDescription(T, Logger) - Method in class ReportFeature
featureDescription(MarksInitialization, Logger) - Method in class ReportFeatureOnMark
featureDescription(MarksInitialization, Logger) - Method in class ReportFeatureOnMarks
featureDescription(MarksInitialization, Logger) - Method in class ReportFeatureOnObjectsBase
featureDescription(MarksInitialization, Logger) - Method in class ReportFeatureWrapError
featureDescription(DeserializedManifest, Logger) - Method in class NumberMarksFromManifest
featureDescription(DeserializedManifest, Logger) - Method in class RootFilePathRegEx
featureDescription(DeserializedManifest, Logger) - Method in class TextFileAsIntegerFromManifest
featureDescription(DeserializedManifest, Logger) - Method in class TextFileAsIntegerFromPath
FeatureEnergy<T extends FeatureInputEnergy> - Class in org.anchoranalysis.image.feature.bean: A base class for features that only require an input that extends from FeatureInputEnergy
FeatureEnergy() - Constructor for class FeatureEnergy
FeatureEnergyChannel - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: A feature that uses a channel from the energy-stack as identified by an index
FeatureEnergyChannel() - Constructor for class FeatureEnergyChannel
FeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a feature and provides a means to calculate inputs for it, a session.
FeatureEvaluator() - Constructor for class FeatureEvaluator
FeatureExporter<S> - Class in org.anchoranalysis.plugin.image.task.feature: Shared-state for an ExportFeatures task.
FeatureExporter(FeatureOutputMetadata, Supplier<S>, FeatureExporterContext) - Constructor for class FeatureExporter: Creates the shared state.
FeatureExporterContext - Class in org.anchoranalysis.plugin.image.task.feature
FeatureExporterContext(InputOutputContext, boolean, boolean, boolean) - Constructor for class FeatureExporterContext
FeatureFromList<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A base class for a Feature that is a function of the results from a list of other features.
FeatureFromList(FeatureList<T>) - Constructor for class FeatureFromList: Create from a list of features.
FeatureFromList() - Constructor for class FeatureFromList
FeatureGeneric<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: Base class for features that broadly accept any type of feature-input.
FeatureGeneric() - Constructor for class FeatureGeneric
FeatureHistogram - Class in org.anchoranalysis.image.feature.bean: A base class for features that accept a histogram as input.
FeatureHistogram() - Constructor for class FeatureHistogram
FeatureHistogramStatistic - Class in org.anchoranalysis.image.feature.bean.histogram: Base class for FeatureHistogram implementations that calculate a statistic from the Histogram.
FeatureHistogramStatistic() - Constructor for class FeatureHistogramStatistic
FeatureImageMetadata - Class in org.anchoranalysis.image.feature.bean: A base class for a feature that accepts a FeatureInputImageMetadata as input.
FeatureImageMetadata() - Constructor for class FeatureImageMetadata
FeatureInitialization - Class in org.anchoranalysis.feature.initialization: Parameters used to initialize a Feature before any calculation occurs.
FeatureInitialization() - Constructor for class FeatureInitialization: Create without any dictionary, energy-stack or shared-objects.
FeatureInitialization(SharedObjects) - Constructor for class FeatureInitialization: Create only with shared-objects.
FeatureInitialization(Dictionary) - Constructor for class FeatureInitialization: Create only with a dictionary.
FeatureInitialization(EnergyStack) - Constructor for class FeatureInitialization: Create only with an energy-stack.
FeatureInitialization(Optional<Dictionary>, Optional<EnergyStackWithoutParameters>, Optional<SharedObjects>) - Constructor for class FeatureInitialization
FeatureInput - Interface in org.anchoranalysis.feature.input: A single input used for feature-calculation to produce a result.
FeatureInputAllMemo - Class in org.anchoranalysis.mpp.feature.input
FeatureInputAllMemo(EnergyMemoList, EnergyStack) - Constructor for class FeatureInputAllMemo
FeatureInputDictionary - Interface in org.anchoranalysis.feature.input: A FeatureInputWithResolution that has an optional associated Dictionary.
FeatureInputDimensions - Class in org.anchoranalysis.feature.input: A FeatureInput that exposes the Dimensions of an image or scene.
FeatureInputDimensions() - Constructor for class FeatureInputDimensions
FeatureInputEnergy - Class in org.anchoranalysis.feature.input: A FeatureInputDimensions that has an optional EnergyStack associated with it.
FeatureInputEnergy() - Constructor for class FeatureInputEnergy: Creates without an associated energy-stack.
FeatureInputEnergy(Optional<EnergyStack>) - Constructor for class FeatureInputEnergy
FeatureInputHistogram - Class in org.anchoranalysis.image.feature.input
FeatureInputHistogram(Histogram, Optional<Resolution>) - Constructor for class FeatureInputHistogram
FeatureInputImageMetadata - Class in org.anchoranalysis.image.feature.input: A FeatureInput that provides ImageMetadata.
FeatureInputImageMetadata(ImageMetadata) - Constructor for class FeatureInputImageMetadata
FeatureInputMark - Class in org.anchoranalysis.mpp.feature.bean.mark
FeatureInputMark(Mark, Optional<Dimensions>) - Constructor for class FeatureInputMark
FeatureInputMark(Mark, Dimensions, Dictionary) - Constructor for class FeatureInputMark
FeatureInputMark(Mark, Optional<Dimensions>, Optional<Dictionary>) - Constructor for class FeatureInputMark
FeatureInputMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
FeatureInputMarkCollection(MarkCollection, Optional<Dimensions>) - Constructor for class FeatureInputMarkCollection
FeatureInputNull - Class in org.anchoranalysis.feature.input: A FeatureInput with no associated parameterization.
FeatureInputObjectCollection - Class in org.anchoranalysis.image.feature.input
FeatureInputObjectCollection(ObjectCollection) - Constructor for class FeatureInputObjectCollection
FeatureInputObjectCollection(ObjectCollection, Optional<EnergyStack>) - Constructor for class FeatureInputObjectCollection
FeatureInputOverlappingCircleFixture - Class in org.anchoranalysis.test.feature.plugins.objects
FeatureInputPairMemo - Class in org.anchoranalysis.mpp.feature.input
FeatureInputPairMemo(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack) - Constructor for class FeatureInputPairMemo
FeatureInputPairObjects - Class in org.anchoranalysis.image.feature.input: A pair of objects (first and second) and maybe a merged version of both
FeatureInputPairObjects(ObjectMask, ObjectMask) - Constructor for class FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask, EnergyStack) - Constructor for class FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>) - Constructor for class FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>, Optional<ObjectMask>) - Constructor for class FeatureInputPairObjects
FeatureInputPairObjects(FeatureInputPairObjects) - Constructor for class FeatureInputPairObjects
FeatureInputResults - Class in org.anchoranalysis.feature.input: A FeatureInput with the stored results from a prior feature-calculation.
FeatureInputResults(ResultsVectorList, FeatureNameMapToIndex) - Constructor for class FeatureInputResults
FeatureInputSingleMemo - Class in org.anchoranalysis.mpp.feature.input
FeatureInputSingleMemo(VoxelizedMarkMemo, EnergyStack) - Constructor for class FeatureInputSingleMemo
FeatureInputSingleMemo(VoxelizedMarkMemo, Optional<EnergyStack>) - Constructor for class FeatureInputSingleMemo
FeatureInputSingleObject - Class in org.anchoranalysis.image.feature.input: An input representing a single object-mask (with maybe an energy-stack associated)
FeatureInputSingleObject(ObjectMask) - Constructor for class FeatureInputSingleObject
FeatureInputSingleObject(ObjectMask, EnergyStack) - Constructor for class FeatureInputSingleObject
FeatureInputSingleObject(ObjectMask, Optional<EnergyStack>) - Constructor for class FeatureInputSingleObject
FeatureInputStack - Class in org.anchoranalysis.image.feature.input
FeatureInputStack() - Constructor for class FeatureInputStack: Should only be used if it's guaranteed the energy stack will be added later, as this this required.
FeatureInputStack(EnergyStackWithoutParameters) - Constructor for class FeatureInputStack
FeatureInputStack(Optional<EnergyStackWithoutParameters>) - Constructor for class FeatureInputStack
FeatureInputType - Class in org.anchoranalysis.feature.input: Performs checks and aggregations on feature-input types are compatible with others
FeatureInputWithResolution - Interface in org.anchoranalysis.feature.input: A FeatureInput that exposes the Resolution of an image or scene.
FeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
FeatureIntersectingObjects() - Constructor for class FeatureIntersectingObjects
FeatureIntersectingObjectsSingleElement - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
FeatureIntersectingObjectsSingleElement() - Constructor for class FeatureIntersectingObjectsSingleElement
FeatureIntersectingObjectsThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
FeatureIntersectingObjectsThreshold() - Constructor for class FeatureIntersectingObjectsThreshold
FeatureList<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: A list of features with the same input-type.
FeatureList() - Constructor for class FeatureList: Creates with an empty list.
FeatureList(Stream<Feature<T>>) - Constructor for class FeatureList: Creates a list from a stream.
FeatureList(List<Feature<T>>) - Constructor for class FeatureList: Wraps an existing list.
FeatureListCSVGeneratorHorizontal - Class in org.anchoranalysis.feature.io.csv: CSV file where each feature is a column (spanning horizontally).
FeatureListCSVGeneratorHorizontal(String, FeatureNameList) - Constructor for class FeatureListCSVGeneratorHorizontal: Creates without setting any results (i.e.
FeatureListCSVGeneratorVertical - Class in org.anchoranalysis.feature.io.csv: CSV file where each feature is a row (spanning vertically).
FeatureListCSVGeneratorVertical(String, FeatureNameList) - Constructor for class FeatureListCSVGeneratorVertical: Creates without setting any results (i.e.
FeatureListEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a list of features and provides a means to calculate inputs for it, a session.
FeatureListEvaluator() - Constructor for class FeatureListEvaluator
FeatureListFactory - Class in org.anchoranalysis.feature.bean.list: Factory for creating FeatureList in different ways.
FeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Provides a list of Features with identical input-type.
FeatureListProvider() - Constructor for class FeatureListProvider
FeatureListProviderAggregatePair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
FeatureListProviderAggregatePair() - Constructor for class FeatureListProviderAggregatePair
FeatureListProviderLDAClassifier<T extends FeatureInput> - Class in org.anchoranalysis.plugin.ml.bean.classifier
FeatureListProviderLDAClassifier() - Constructor for class FeatureListProviderLDAClassifier
FeatureListProviderSVMClassifier - Class in org.anchoranalysis.plugin.ml.bean.classifier
FeatureListProviderSVMClassifier() - Constructor for class FeatureListProviderSVMClassifier
FeatureMark - Class in org.anchoranalysis.mpp.feature.bean.mark
FeatureMark() - Constructor for class FeatureMark
FeatureMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
FeatureMarkCollection() - Constructor for class FeatureMarkCollection
FeatureMarkDirection - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
FeatureMarkDirection() - Constructor for class FeatureMarkDirection
FeatureMarkRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
FeatureMarkRegion() - Constructor for class FeatureMarkRegion
FeatureNameList - Class in org.anchoranalysis.feature.name: A list of Strings representing feature names.
FeatureNameList() - Constructor for class FeatureNameList: Create with no names (an empty list).
FeatureNameList(Stream<String>) - Constructor for class FeatureNameList: Create from a stream of names.
FeatureNameList(List<String>) - Constructor for class FeatureNameList
FeatureNameMapToIndex - Class in org.anchoranalysis.feature.name: A map of feature-names (strings) to indexes (int).
FeatureNameMapToIndex() - Constructor for class FeatureNameMapToIndex
featureNames() - Method in class NamedFeatureStore: The names of all Features in the store, in identical order to the store.
featureNamesNonAggregate() - Method in class FeatureOutputMetadata: Names of each feature in the feature columns.
FeatureObjectCollection - Class in org.anchoranalysis.image.feature.bean.object.collection: A base class for a feature that accepts a ObjectCollection as input.
FeatureObjectCollection() - Constructor for class FeatureObjectCollection
FeatureOutputMetadata - Class in org.anchoranalysis.feature.io.results: Additional information needed for the outputs in FeatureCalculationResults.
FeatureOutputMetadata(LabelHeaders, FeatureNameList, FeatureOutputNames) - Constructor for class FeatureOutputMetadata
FeatureOutputNames - Class in org.anchoranalysis.feature.io.results: The customizable output names used by FeatureCalculationResults, which all follow a pattern based on a prefix.
FeatureOutputNames() - Constructor for class FeatureOutputNames: Creates using default names, equivalent to a prefix of features.
FeatureOutputNames(String, boolean, boolean) - Constructor for class FeatureOutputNames: Creates output-names based upon a prefix.
FeaturePairMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
FeaturePairMemo() - Constructor for class FeaturePairMemo
FeaturePairMemoOne - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
FeaturePairMemoOne() - Constructor for class FeaturePairMemoOne
FeaturePairMemoSingleRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
FeaturePairMemoSingleRegion() - Constructor for class FeaturePairMemoSingleRegion
FeaturePairObjects - Class in org.anchoranalysis.image.feature.bean.object.pair
FeaturePairObjects() - Constructor for class FeaturePairObjects
FeatureProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider: Provides a single Feature.
FeatureProvider() - Constructor for class FeatureProvider
FeatureProviderBean<B,P> - Class in org.anchoranalysis.feature.bean.provider: Base class for FeatureRelatedBeans that implement Provider to provide an object of type S.
FeatureProviderBean() - Constructor for class FeatureProviderBean
FeatureProviderDefine<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider: Defines a single Feature to provide via a bean property.
FeatureProviderDefine() - Constructor for class FeatureProviderDefine
FeatureProviderDefine(Feature<T>) - Constructor for class FeatureProviderDefine
FeatureProviderReference - Class in org.anchoranalysis.feature.bean.provider: Provides an existing Feature identified by its name and optionally a feature-list in which is resides.
FeatureProviderReference() - Constructor for class FeatureProviderReference
FeatureRelatedBean<T> - Class in org.anchoranalysis.feature.bean: Beans-related to Features, and which require initialization with FeatureRelatedInitialization.
FeatureRelatedBean() - Constructor for class FeatureRelatedBean: Create with default initializers.
FeatureRelatedInitialization - Class in org.anchoranalysis.feature.initialization: Parameters for initializing a FeatureRelatedBean.
FeatureResults - Class in org.anchoranalysis.feature.bean.results: Features that process ResultsVectorList.
FeatureResults() - Constructor for class FeatureResults
FeatureResultsAndThumbnails - Class in org.anchoranalysis.plugin.image.task.feature: A collection of results from feature calculation, and associated thumbnails.
FeatureResultsAndThumbnails(FeatureOutputMetadata, FeatureExporterContext) - Constructor for class FeatureResultsAndThumbnails
FeatureResultsStatistic - Class in org.anchoranalysis.feature.bean.results: Base class for an instance of FeatureResults that calculating a statistic across all results in the ResultsVectorList for a particular feature-value.
FeatureResultsStatistic() - Constructor for class FeatureResultsStatistic
FeatureResultSupplier - Interface in org.anchoranalysis.plugin.operator.feature.statistics: Supplies the result of a feature-calculation
features() - Method in class NamedFeatureStore: All Features in the store, in identical order.
FeatureSession - Class in org.anchoranalysis.feature.session: A single-point in the code for creating feature-sessions (a factory).
FeaturesFromXmlFixture - Class in org.anchoranalysis.test.feature.plugins
FeatureSingleMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
FeatureSingleMemo() - Constructor for class FeatureSingleMemo
FeatureSingleMemoRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
FeatureSingleMemoRegion() - Constructor for class FeatureSingleMemoRegion
FeatureSingleObject - Class in org.anchoranalysis.image.feature.bean.object.single
FeatureSingleObject() - Constructor for class FeatureSingleObject
FeatureSingleObjectFromShared<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates as object-masks from entities in shared, using the feature-input only for a energy-stack.
FeatureSingleObjectFromShared() - Constructor for class FeatureSingleObjectFromShared
featuresInitialization() - Method in class ImageInitialization
FeatureSource<T extends InputFromManager,S,U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Extracts features from some kind of inputs to produce one or more rows in a feature-table.
FeatureSource() - Constructor for class FeatureSource
FeatureStack - Class in org.anchoranalysis.image.feature.bean
FeatureStack() - Constructor for class FeatureStack
FeatureSymbolCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Resolves and calculates a feature by a symbol.
FeatureTableCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.image.feature.calculator: A feature-calculator with additional functions for encoding the output in in a tabular-format with column-names.
FeatureTableCSVGenerator<T> - Class in org.anchoranalysis.feature.io.csv: Base class for a Generator that outputs a feature-table in CSV format.
FeatureTableCSVGenerator(String, List<String>) - Constructor for class FeatureTableCSVGenerator: Creates for a particular manifest-function and headers.
FeatureTestCalculator - Class in org.anchoranalysis.test.feature.plugins
FeatureTestCalculatorDuo - Class in org.anchoranalysis.test.feature.plugins: Tests that consider two possibilities: positive and negative
featureToCalcInputVal() - Method in class CompareWithRange
featureToCalcInputVal() - Method in class CompareWithRangeFeature
featureToCalcInputVal() - Method in class IfConditionWithinRange
featureToCalcInputVal() - Method in class IfOutsideRange
featureToCalcInputVal() - Method in class RangeCompareBase: Which feature to calculate the input-value? The result is then passed to RangeCompareBase.calculateForValue(double, org.anchoranalysis.feature.calculate.FeatureCalculationInput<T>)
FeatureUnary<T extends FeatureInput,S extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A feature that contains another feature as a bean-parameter.
FeatureUnary() - Constructor for class FeatureUnary
FeatureUnary(Feature<S>) - Constructor for class FeatureUnary
FeatureUnaryGeneric<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A FeatureUnary that accepts any FeatureInput irrespective of type.
FeatureUnaryGeneric(Feature<T>) - Constructor for class FeatureUnaryGeneric: Create with a specific feature, that provides the input to the unary function.
FeatureUnaryGeneric() - Constructor for class FeatureUnaryGeneric
FeatureValueCheckMark<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.bean.check
FeatureValueCheckMark() - Constructor for class FeatureValueCheckMark
FeatureValueIndividualEnergyGreaterThan - Class in org.anchoranalysis.plugin.mpp.bean.check
FeatureValueIndividualEnergyGreaterThan() - Constructor for class FeatureValueIndividualEnergyGreaterThan
FeatureValueMarkGreaterEqualThan - Class in org.anchoranalysis.plugin.mpp.bean.check
FeatureValueMarkGreaterEqualThan() - Constructor for class FeatureValueMarkGreaterEqualThan
FeedbackBeginParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
FeedbackBeginParameters() - Constructor for class FeedbackBeginParameters
FeedbackEndParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
FeedbackEndParameters(T, MessageLogger) - Constructor for class FeedbackEndParameters
FeedbackReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback
FeedbackReceiverBean<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
FeedbackReceiverBean() - Constructor for class FeedbackReceiverBean
FeedbackReceiverList<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
FeedbackReceiverList() - Constructor for class FeedbackReceiverList
FeedbackReceiverRequireArguments<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
FeedbackReceiverRequireArguments() - Constructor for class FeedbackReceiverRequireArguments
fetchUnmatchedWorker() - Method in class HungarianAlgorithm
FieldAccessor - Class in org.anchoranalysis.bean: Utilities to access a Field of an AnchorBean.
fieldFromBean(AnchorBean<?>, Field) - Static method in class FieldAccessor: Retrieves the value of a Field from a AnchorBean.
fields() - Method in class AnchorBean: A list of all bean-fields that are associated with this bean directly (fields of children are not checked).
FileDetails - Class in org.anchoranalysis.plugin.io.multifile
FileDetails(Path, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Constructor for class FileDetails
fileExtensionWriter(OutputWriteSettings, StackWriteOptions, Optional<Logger>) - Static method in class GeneratorOutputter
FileFormat - Interface in org.anchoranalysis.core.format: A file-format that is read or written to the filesystem.
fileFormat(StackWriteOptions) - Method in class OneOrThreeChannelsWriter
fileFormat(StackWriteOptions) - Method in class StackWriter: The file format that will be written by the generator.
fileFormat(StackWriteOptions) - Method in class OMETiff
fileFormat(StackWriteOptions) - Method in class OMEXML
fileFormat(StackWriteOptions) - Method in class Tiff
fileFormat(StackWriteOptions) - Method in class PNG
fileFormat(StackWriteOptions) - Method in class Tiff
fileFormat(StackWriteOptions) - Method in class StackWriterDelegateBase
fileFormat(StackWriteOptions) - Method in class WriteResolutionXml
FileFormatFactory - Class in org.anchoranalysis.core.format: Creates a FileFormat from a string.
fileFormatWarnUnexpected(StackWriteOptions, Optional<Logger>) - Method in class StackWriter: The file format that will be written by the generator, warning with a log message if different to suggestion.
FileInput - Class in org.anchoranalysis.io.input.file: An input pertaining to a single file on the file-system.
FileInput(NamedFile) - Constructor for class FileInput
fileInputManager() - Method in class QuickBase
FileLabelMap<T> - Class in org.anchoranalysis.plugin.image.task.labeller
FileMatch - Class in org.anchoranalysis.io.manifest.finder.match
filenameFromOutputFormatString(String, String) - Method in class IndexableOutputNameStyle: Constructs a full name from the output format string and an index
filenameFromOutputFormatString(String, String) - Method in class IntegerSuffixOutputNameStyle
filenameFromOutputFormatString(String, String) - Method in class StringSuffixOutputNameStyle
FileNamer - Class in org.anchoranalysis.io.input.bean.namer: Associates a name (a compact unique identifier) with a file.
FileNamer() - Constructor for class FileNamer
FileNamerContext - Class in org.anchoranalysis.io.input.file: Provides useful additional objects when assigning a name to a file.
FileNamerContext(Logger) - Constructor for class FileNamerContext
FileNamerContext(Optional<Path>, boolean, Optional<IndexRangeNegative>, Logger) - Constructor for class FileNamerContext
FileNamerContext(String, Logger) - Constructor for class FileNamerContext
FileNamerContext(Optional<Path>, boolean, String, Optional<IndexRangeNegative>, Logger) - Constructor for class FileNamerContext
FileNamerIndependent - Class in org.anchoranalysis.io.input.bean.namer: Base class for methods that derive the name independently for each file.
FileNamerIndependent() - Constructor for class FileNamerIndependent
FilenameSplitExtension - Class in org.anchoranalysis.core.system.path: A file-name with the base (without extension) split from the extension.
FilenameSplitExtension(String, Optional<String>) - Constructor for class FilenameSplitExtension: Creates from a path without an extension.
filenameWithoutExtension(File) - Static method in class ExtensionUtilities: Retrieves filename from a File but without any extension.
filenameWithoutExtension(int) - Method in class IndexableOutputNameStyle: Like IndexableOutputNameStyle.filenameWithoutExtension() but incorporates an integer index.
filenameWithoutExtension(String) - Method in class IndexableOutputNameStyle: Like IndexableOutputNameStyle.filenameWithoutExtension() but incorporates an string index.
filenameWithoutExtension() - Method in class IndexableOutputNameStyle
filenameWithoutExtension() - Method in class OutputNameStyle: The filename to be written, including prefix, suffix, etc.
filenameWithoutExtension() - Method in class SimpleOutputNameStyle
filenameWithoutExtension() - Method in class WithoutOutputNameStyle
filePath() - Method in class MultiInput
FilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
FilePath() - Constructor for class FilePath
FilePathAppendBase - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
FilePathAppendBase() - Constructor for class FilePathAppendBase
FilePathBaseAppendToManager - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
FilePathBaseAppendToManager() - Constructor for class FilePathBaseAppendToManager
FilePathBaseAppendToManagerWithFileID - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
FilePathBaseAppendToManagerWithFileID() - Constructor for class FilePathBaseAppendToManagerWithFileID
FilePathBean<T> - Class in org.anchoranalysis.bean.shared.path: Base class for beans that require initialization with FilePathInitialization.
FilePathBean() - Constructor for class FilePathBean
filePathDifference(Path, Path) - Static method in class PathOperations: Finds the difference between a path and a base.
FilePathInitialization - Class in org.anchoranalysis.bean.shared.path: Initialization parameters for a named-set of file-paths.
FilePathInitialization(SharedObjects) - Constructor for class FilePathInitialization: Creates using a SharedObjects to create a NamedProviderStore for the file-paths.
FilePathParser - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
FilePathParser() - Constructor for class FilePathParser
FilePathPattern - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Converts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library.
FilePathPattern(String...) - Constructor for class FilePathPattern: Create with one or more paths.
FilePathPattern() - Constructor for class FilePathPattern
FilePathProvider - Class in org.anchoranalysis.io.input.bean.path.provider: Base class for beans that implement Provider to provide a Path.
FilePathProvider() - Constructor for class FilePathProvider
FilePathProviderReference - Class in org.anchoranalysis.io.input.bean.path.provider
FilePathProviderReference() - Constructor for class FilePathProviderReference
filePaths() - Method in class ImageInitialization
FilePathToUnixStyleConverter - Class in org.anchoranalysis.core.system.path: Conversion to Unix-style separators.
FileSetFromStringSet - Class in org.anchoranalysis.plugin.io.bean.file.provider
FileSetFromStringSet() - Constructor for class FileSetFromStringSet
FileSizeStatistics - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Tracks the range of file-size.
FileSizeStatistics() - Constructor for class FileSizeStatistics
FilesProvider - Class in org.anchoranalysis.io.input.bean.files
FilesProvider() - Constructor for class FilesProvider
FilesProviderException - Exception in org.anchoranalysis.io.input.file
FilesProviderException(String) - Constructor for exception FilesProviderException
FilesProviderException(Throwable) - Constructor for exception FilesProviderException
FilesProviderUnary - Class in org.anchoranalysis.io.input.bean.files: Like FilesProvider but employs a unary operator on a call to an existing FilesProvider.
FilesProviderUnary() - Constructor for class FilesProviderUnary
FilesProviderWithDirectory - Class in org.anchoranalysis.io.input.bean.files: Base class for implementations of FilesProvider which do have an associated directory.
FilesProviderWithDirectory() - Constructor for class FilesProviderWithDirectory
FilesProviderWithDirectoryString - Class in org.anchoranalysis.io.input.bean.files: A FilesProviderWithDirectory where the directory is optionally specified as a string constant
FilesProviderWithDirectoryString() - Constructor for class FilesProviderWithDirectoryString
FilesProviderWithDirectoryUnary - Class in org.anchoranalysis.io.input.bean.files: Like FilesProviderWithDirectory but employs a unary operator on a call to an existing FilesProviderWithDirectory.
FilesProviderWithDirectoryUnary() - Constructor for class FilesProviderWithDirectoryUnary
FilesProviderWithoutDirectory - Class in org.anchoranalysis.io.input.bean.files: Base class for implementations of FilesProvider which do not have an associated directory.
FilesProviderWithoutDirectory() - Constructor for class FilesProviderWithoutDirectory
FileType - Class in org.anchoranalysis.io.manifest.file
FileType(ManifestDescription, String) - Constructor for class FileType
FileWithDirectoryInput - Class in org.anchoranalysis.io.input.file: An input pertaining to a single file on the file-system - and a directory in which it resides.
FileWithDirectoryInput(NamedFile, Path) - Constructor for class FileWithDirectoryInput: Create for a particular file and directory.
fill(BinaryVoxels<UnsignedByteBuffer>) - Static method in class ApplyImageJMorphologicalOperation
Filled - Class in org.anchoranalysis.image.io.bean.object.draw: Draws a filled-in shape for each object.
Filled() - Constructor for class Filled
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider
FillHoles() - Constructor for class FillHoles
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.object.provider: Fills holes in an object.
FillHoles() - Constructor for class FillHoles
filter(Stream<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class CheckedStream: Performs a Stream.filter(java.util.function.Predicate<? super T>) but accepts a predicate that can throw a checked-exception.
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class ObjectFilter: Filters an ObjectCollection to remove objects.
filter(Predicate<ObjectMask>) - Method in class ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate
filter(CheckedPredicate<ObjectMask, E>, Optional<ObjectCollection>) - Method in class ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate - and optionally store rejected objects.
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class And
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class Or
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class ObjectFilterPredicate
Filter - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Filter() - Constructor for class Filter
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class ObjectCollectionProviderFilterBase
Filter - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies an object-filter to the results of an upstream segmentation.
Filter() - Constructor for class Filter
filterAndMap(Predicate<Feature<T>>, CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class FeatureList: Filters inputs and then performs a FeatureList.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.feature.bean.Feature<T>, org.anchoranalysis.feature.bean.Feature<S>, E>).
filterAndMap(Predicate<ObjectMask>, UnaryOperator<ObjectMask>) - Method in class ObjectMaskStream: Performs a ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>).
filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectWithProperties, E>) - Static method in class ObjectCollectionWithPropertiesFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectWithProperties.
filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
filterAndMapToList(List<S>, Predicate<S>, CheckedFunction<S, T, E>) - Static method in class FunctionalList: Creates a new collection by filtering a list and then mapping to a list of another type.
filterAndMapWithIndexFrom(List<T>, Predicate<T>, CheckedBiFunction<T, Integer, ObjectMask, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by filtering a list and then mapping from it to ObjectMask.
filterAndMapWithIndexToList(List<S>, Predicate<S>, CheckedBiFunction<S, Integer, T, E>) - Static method in class FunctionalList: Creates a new collection by filtering a list and then mapping (with an index) to a list of another type.
FilterByGroup - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
FilterByGroup() - Constructor for class FilterByGroup
FilterCSVColumn<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Finds a CSV file with the names of an input as the first-column.
FilterCSVColumn() - Constructor for class FilterCSVColumn
FilterDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters all the input objects for only those with certain types of descriptive-names.
FilterDescriptiveName() - Constructor for class FilterDescriptiveName
FilterDescriptiveNameEqualsContains - Class in org.anchoranalysis.plugin.io.input.filter: Filters a list of input-objects by the descriptive name
FilterDescriptiveNameEqualsContains(String, String) - Constructor for class FilterDescriptiveNameEqualsContains
filterExclude(Predicate<ObjectMask>) - Method in class ObjectMaskStream: Filters a ObjectCollection to exclude certain items based on a predicate
FilterForExistingFiles - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
FilterForExistingFiles() - Constructor for class FilterForExistingFiles
FilterHelper - Class in org.anchoranalysis.plugin.imagej.channel.provider
FilterIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters a list of inputs when in debug-mode
FilterIfDebug() - Constructor for class FilterIfDebug
filterSubset(Predicate<ObjectMask>, Collection<Integer>) - Method in class ObjectMaskStream: Like ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) but only operates on certain indices of the collection.
filterSubsetStream(Predicate<ObjectMask>, Collection<Integer>) - Method in class ObjectMaskStream: Like ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection.
filterToList(Collection<T>, Predicate<T>) - Static method in class FunctionalList: Filters a collection and maps the result to a list.
filterToList(Collection<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class FunctionalList: Filters a collection and maps the result to a list.
FilterWithRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Rejects files that fail to match a particular regular-expression
FilterWithRegularExpression() - Constructor for class FilterWithRegularExpression
Findable<T> - Interface in org.anchoranalysis.annotation.io.image.findable: Parent class for an element that exists in one of two-states, either Found or NotFound.
findAllNonInputFiles() - Method in class InputsWithDirectory: Find all files in the input directory are not used as inputs.
findArbitraryOnVoxel() - Method in class ObjectMask: Finds any arbitrary on voxel on the object.
findClosestResult(Point3i) - Method in class LevelResultCollection
FindCommonVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Finds a common voxel-data type to represent two types.
FindContour - Class in org.anchoranalysis.image.core.contour: Finds contour voxels, the pixels forming a continuous path along the boundary of the object or mask.
findConvertedInputFor(NamedChannelsInput, MessageLogger) - Method in class SharedStateRememberConverted: Finds a converted-input that has been remembered.
findDirectory(List<MutableDirectory>, Predicate<MutableDirectory>) - Method in class MutableDirectory
findDirectoryWithName(Metadata, Class<T>, String) - Static method in class ReadMetadataUtilities: Finds the first Directory in the metadata with type directoryType and whose name is equal to directoryName.
Finder - Interface in org.anchoranalysis.io.manifest.finder
FinderDictionary - Class in org.anchoranalysis.io.manifest.finder
FinderDictionary(String, ErrorReporter) - Constructor for class FinderDictionary
FinderExperimentFileDirectories - Class in org.anchoranalysis.io.manifest.finder
FinderExperimentFileDirectories() - Constructor for class FinderExperimentFileDirectories
FinderFileAsText - Class in org.anchoranalysis.io.manifest.finder
FinderFileAsText(String, ErrorReporter) - Constructor for class FinderFileAsText
finderForGrandchild() - Method in class CheckCacheForSpecificChildren
finderForGrandchild() - Method in interface ChildCacheFinder: What finder to use for children-of-children?
finderForGrandchild() - Method in class DefaultChildCacheFinder
FinderSerializedObject<T> - Class in org.anchoranalysis.io.manifest.finder
FinderSerializedObject(String, Logger) - Constructor for class FinderSerializedObject
FinderSingleDirectory - Class in org.anchoranalysis.io.manifest.finder
FinderSingleDirectory() - Constructor for class FinderSingleDirectory
FinderSingleFile - Class in org.anchoranalysis.io.manifest.finder
FinderSingleFile(ErrorReporter) - Constructor for class FinderSingleFile
FinderUtilities - Class in org.anchoranalysis.io.manifest.finder
FindFailedException - Exception in org.anchoranalysis.io.manifest.finder
FindFailedException(String) - Constructor for exception FindFailedException
FindFailedException(Throwable) - Constructor for exception FindFailedException
findFieldsOfClass(Class<?>) - Method in class AnchorBean: Finds all bean-fields that are instances of a certain class.
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class JobRootDirectory
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class MutableDirectory
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class RootDirectory
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class Subdirectory
findFile(Manifest) - Method in class FinderDictionary
findFile(Manifest) - Method in class FinderFileAsText
findFile(Manifest) - Method in class FinderSerializedObject
findFile(Manifest) - Method in class FinderSingleFile
findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in class MutableDirectory
findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in interface SequencedDirectory
FindFilesException - Exception in org.anchoranalysis.io.input.path.matcher
FindFilesException(String) - Constructor for exception FindFilesException
findListDirectory(Manifest, Predicate<MutableDirectory>) - Static method in class FinderUtilities
findListFile(Manifest, Predicate<OutputtedFile>) - Static method in class FinderUtilities
findMatch(ObjectCollection) - Method in class ObjectMatcher: Finds matches for objects
findMatch(ObjectCollection) - Method in class Always
findMatch(ObjectCollection) - Method in class Bridge
findMatch(ObjectCollection) - Method in class Intersection
FindMatchingFiles - Class in org.anchoranalysis.io.input.path.matcher
FindMatchingFiles(boolean, Optional<Progress>) - Constructor for class FindMatchingFiles
FindMatchingFiles() - Constructor for class FindMatchingFiles
findMatchingFiles(Path, PathMatchConstraints, Optional<Logger>) - Method in class FindMatchingFiles
findMaxPriority() - Method in class MergeGraph
FindMinimumDistance - Class in org.anchoranalysis.plugin.mpp.contour.distance: Finds the minimum distance of a point among any ContiguousVoxelPath's head and tail points.
findMostDeepCombinableException() - Method in exception AnchorCombinableException: Traverses through the nested-exceptions and finds the most deep exception that is combinable.
findObjectsMatchingRow(CSVRow, IntersectingObjects<ObjectMask>) - Method in class ColumnDefinition
findObjectsMatchingRow(CSVRow, IntersectingObjects<ObjectMask>) - Method in class Pairwise
findObjectsMatchingRow(CSVRow, IntersectingObjects<ObjectMask>) - Method in class Single
findObjectsMatchingRow(IntersectingObjects<ObjectMask>) - Method in class CSVRow
findOptimum(KernelProposer<U, V>, V, FeedbackReceiver<S>, OptimizationContext) - Method in class OptimizationScheme: Finds an optimal state using kernel proposals.
findOptimum(KernelProposer<U, UpdatableMarksList>, UpdatableMarksList, FeedbackReceiver<S>, OptimizationContext) - Method in class SimulatedAnnealing
findOptimum(KernelProposer<S, V>, V, FeedbackReceiver<S>, OptimizationContext) - Method in class UniformProposal
FindPointOnContour - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.contour: Finds a pixel in a particular direction on the exterior outer contour of an object.
FindPointOnContour() - Constructor for class FindPointOnContour
FindPointOnContourWalk - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.contour: Walks incrementally in a particular direction until the contour is found.
FindPointOnContourWalk() - Constructor for class FindPointOnContourWalk
findRoot(String, boolean) - Method in class RootPathMap: Finds a root to match a name and debug/status
findSingleItem(Manifest, Predicate<OutputtedFile>) - Static method in class FinderUtilities
First - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates the first-object in a pair only
First(Feature<FeatureInputSingleObject>) - Constructor for class First
First() - Constructor for class First
first() - Method in class MultiLevelRecordedOutputs: For recording first-level outputs.
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class BinaryKernelMorphological: The first check done on the kernel center-point, before checking any neighbors.
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class DilationKernel
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class ErosionKernel
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class OutlineKernelBase
firstLevelContains(String) - Method in class OutputEnableRulesSpecify
firstPart() - Method in class CombinedName
firstPart() - Method in interface MultiName: The first part, and grouping key.
firstPart() - Method in class SimpleName
firstPart() - Method in class FilePathAppendBase
firstPartWithCustomMiddle(String) - Method in class FilePathAppendBase
firstPartWithDataset() - Method in class FilePathAppendBase: The first-part of the out-path string including the dataset of the current experiment as a folder
firstPartWithFilename() - Method in class FilePathAppendBase: The first-part of the out-path string including the file-name of the previous experiment as a folder
fit(List<Point3f>, Mark, Dimensions) - Method in class PointsFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class LinearLeastSquaresEllipseFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class LinearLeastSquaresEllipsoidFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class LinearLeastSquaresViaNormalEquationBase
fit(List<Point3f>, Mark, Dimensions) - Method in class Reference
fit(List<Point3f>, Mark, Dimensions) - Method in class ReflectInAxesWithinDistance
FitBoxToOnVoxels - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Fits a box around the on voxels.
FitBoxToOnVoxels() - Constructor for class FitBoxToOnVoxels
fitMarkToPointsFromMarks(MarkCollection, Dimensions) - Method in class CreateMarkFromPoints: Extract points from a marks, creates a new mark from markProvider and then fits this mark the extracted points
FitPoints - Class in org.anchoranalysis.plugin.points.bean
FitPoints() - Constructor for class FitPoints
FitPointsFromObjects - Class in org.anchoranalysis.plugin.points.bean
FitPointsFromObjects() - Constructor for class FitPointsFromObjects
fitPointsToMark(List<Point3f>, Mark, Dimensions) - Method in class PointsFitterToMark
FitResult - Class in org.anchoranalysis.plugin.points.bean.fitter
FitResult() - Constructor for class FitResult
FitTo - Class in org.anchoranalysis.plugin.image.bean.scale: Scales an image to approximately similar in size to a SizeXY.
FitTo() - Constructor for class FitTo
flagForNoRegion() - Static method in class RegionMembershipUtilities
flagForRegion(int) - Static method in class RegionMembershipUtilities
flagForRegion(int, int) - Static method in class RegionMembershipUtilities: Combines two regions
flagForRegion(int, int, int) - Static method in class RegionMembershipUtilities: Combines three regions
flags() - Method in class RegionMembership
flatMap(Stream<S>, Class<? extends Exception>, CheckedFunction<S, Collection<? extends T>, E>) - Static method in class CheckedStream: Performs a Stream.flatMap(java.util.function.Function<? super T, ? extends java.util.stream.Stream<? extends R>>) but accepts a function that can throw a checked-exception
flatMap(Optional<S>, CheckedFunction<S, Optional<T>, E>) - Static method in class OptionalUtilities: Like Optional.flatMap(java.util.function.Function<? super T, java.util.Optional>) but tolerates an exception in the mapping function, which is immediately thrown.
flatMap(Function<ObjectMask, ObjectCollection>) - Method in class ObjectMaskStream: Creates a new ObjectCollection after mapping each item to several others.
flatMap(Class<? extends Exception>, CheckedFunction<ObjectMask, ObjectCollection, E>) - Method in class ObjectMaskStream: Like a typical flatMap() operation but accepts a mapping function that throws a checked exception.
flatMapFrom(Collection<T>, Function<T, ObjectCollection>) - Static method in class ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection.
flatMapFrom(Stream<T>, Class<? extends Exception>, CheckedFunction<T, ObjectCollection, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
flatMapFromCollection(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Collection<? extends ObjectMask>, E>) - Static method in class ObjectCollectionFactory: Creates a new ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> and rethrowing any exception during mapping.
flatMapFromOptional(Iterable<S>, CheckedFunction<S, Optional<FeatureList<T>>, E>) - Static method in class FeatureListFactory: Creates a new feature-list by flat-mapping an iterable to an optional feature
flatMapFromRange(int, int, IntFunction<ObjectCollection>) - Static method in class ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
flatMapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectCollection, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
flatMapToList(Collection<S>, Function<S, Stream<T>>) - Static method in class FunctionalList: Flat-maps a collection to a list where in the original collection can produce many elements in the outgoing list.
Flatten - Class in org.anchoranalysis.image.io.bean.object.draw: Performs a flattening (maximum intensity projection in each channel) of the output of another writer
Flatten() - Constructor for class Flatten
Flatten(DrawObject) - Constructor for class Flatten
FlattenAsChannel - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Combines all series and frames returned by a reader by converting them into multiple channels in the same image.
FlattenAsChannel() - Constructor for class FlattenAsChannel
FlattenStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Like a StackGenerator but first applies a maximum-intensity-projection.
FlattenStackGenerator(boolean, String) - Constructor for class FlattenStackGenerator
flattenZ() - Method in class Mask: Creates an otherwise identical Mask but a maximum-intensity-projection applied to the z-dimension.
flattenZ() - Method in class ObjectMask: A maximum-intensity projection.
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ() - Constructor for class FlattenZ
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ() - Constructor for class FlattenZ
flattenZ() - Method in class BoundingBox: Collapses the z-dimension of the box to a single voxel depth, and a corner at 0 voxels.
flattenZ() - Method in class Extent: Collapses the Z dimension.
floatArray(float[]) - Static method in class VoxelBufferWrap: Wraps an float-array into a voxel-buffer.
floatBuffer(FloatBuffer) - Static method in class VoxelBufferWrap: Wraps a float buffer into a voxel-buffer.
floatFromDouble(Point2d) - Static method in class PointConverter: Convert a Point2d to a Point2f.
floatFromDouble(Point3d) - Static method in class PointConverter: Convert a Point3d to a Point3f.
floatFromInt(Point2i) - Static method in class PointConverter: Convert a Point2i to a Point3f using 0 as the value of the Z-axis component.
floatFromInt(ReadableTuple3i) - Static method in class PointConverter: Convert a ReadableTuple3i to a Point3f.
floatFromIntDropZ(ReadableTuple3i) - Static method in class PointConverter: Creates a ReadableTuple3i to a Point3f, preserving X- and Y-components but set setting the Z-component to be 0.
floatFromMat(Mat, Extent) - Static method in class VoxelBufferFromMat: Converts a Mat to a VoxelBuffer with voxel data-type FloatBuffer.
FloatFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
FloatFromUnsignedByte() - Constructor for class FloatFromUnsignedByte
FloatFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
FloatFromUnsignedInt() - Constructor for class FloatFromUnsignedInt
FloatUtilities - Class in org.anchoranalysis.math.arithmetic: Utilities for arithmetic operations involving type float.
FloatVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 32-bit voxel data-type representing floating-point numbers, as per the Java primitive float type.
FloodFillEachIntensityLevel - Class in org.anchoranalysis.plugin.imagej.bean.object.segment: Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.
FloodFillEachIntensityLevel() - Constructor for class FloodFillEachIntensityLevel
flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterCreator>, InputOutputContext) - Method in interface FeatureCalculationResults: Writes any queued (but not yet written elements to the file-system), and closes open file-handles.
forBoxes(BoundingBox, BoundingBox) - Static method in class IntersectionOverUnion: Calculates the intersection-over-union score a pair of bounding-boxes.
ForceBitsPerPixel - Class in org.anchoranalysis.io.bioformats.bean.options
ForceBitsPerPixel() - Constructor for class ForceBitsPerPixel
ForceChannelsPerByteArray - Class in org.anchoranalysis.io.bioformats.bean.options
ForceChannelsPerByteArray() - Constructor for class ForceChannelsPerByteArray
ForceNumberChannels - Class in org.anchoranalysis.io.bioformats.bean.options
ForceNumberChannels() - Constructor for class ForceNumberChannels
ForceNumberFrames - Class in org.anchoranalysis.io.bioformats.bean.options
ForceNumberFrames() - Constructor for class ForceNumberFrames
ForceTimeSeriesToStack - Class in org.anchoranalysis.io.bioformats.bean.options: Treats a time-series as if it was a z-stack
ForceTimeSeriesToStack() - Constructor for class ForceTimeSeriesToStack
forChild() - Method in interface FeatureCalculationInput: Performs calculations not on the main cache, but on a child cache.
forChild() - Method in class SessionInputSequential
forEach(Stream<T>, Class<? extends Exception>, CheckedConsumer<T, E>) - Static method in class CheckedStream: Performs a Stream.forEach(java.util.function.Consumer<? super T>) but accepts a consumer that can throw a checked-exception.
forEach(Consumer<RecordedExecutionTimes.RecordedOperation>) - Method in class RecordedExecutionTimes: For each unique operation with a recorded-time, call consumer.
forEach(Consumer<Feature<T>>) - Method in class SharedFeaturesSubset: Iterates over each feature in the instance.
forEach(CheckedBiConsumer<String, StoreSupplier<Stack>, E>) - Method in class NamedStacks: Iterates over each entry in the map.
forEachProperty(BiConsumer<String, Object>) - Method in class ObjectWithProperties: Executes a consumer on each property.
forgetAll() - Method in class SharedStateRememberConverted: Forgets all converted inputs.
format() - Method in class BMP
format() - Method in class HeaderFormat: The associated ImageFileFormat with this header.
format() - Method in class JPEG
format() - Method in class PNG
FormatExtensions - Class in org.anchoranalysis.core.format: File extensions for various formats.
formatter() - Method in enum DateStyle: Derives a formatter for the particular date-style.
ForSpecificAxis<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Dimensions-calculation for one specific axis only.
ForSpecificAxis() - Constructor for class ForSpecificAxis
Found<T> - Class in org.anchoranalysis.annotation.io.image.findable: A positive-result when an object is found at a particular location.
Found(T) - Constructor for class Found
FrequencyMap<T> - Class in org.anchoranalysis.plugin.io.shared: Counts the frequency of certain strings, and describes the contents in human language.
FrequencyMap() - Constructor for class FrequencyMap
FriendlyExceptionCreator - Class in org.anchoranalysis.bean.xml.exception: Converts certain exceptions that occur from XML-Parsing into a friendly form to display to the user.
friendlyMessage() - Method in exception AnchorFriendlyCheckedException
friendlyMessage() - Method in exception AnchorFriendlyRuntimeException
friendlyMessage() - Method in interface HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong.
friendlyMessageHierarchy() - Method in exception AnchorFriendlyCheckedException
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception AnchorFriendlyCheckedException
friendlyMessageHierarchy() - Method in exception AnchorFriendlyRuntimeException
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception AnchorFriendlyRuntimeException
friendlyMessageHierarchy() - Method in interface HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong, which doesn't impose a fixed-size, or showExceptionNames
friendlyMessageHierarchy(Writer, int, boolean) - Method in interface HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong, including all nested exceptions that have a non-empty error message
from(Feature<T>...) - Static method in class FeatureListFactory: Creates a list for one or more features
from(Stack) - Static method in class StackWriteAttributesFactory: The options that narrowly describe a stack as possible.
from(VoxelsUntyped) - Static method in class ConvertToImg: Converts from a VoxelsUntyped (Anchor structure) to a Img (ImgLib2 structure).
from(VoxelsUntyped) - Static method in class ConvertToImagePlus: Creates an ImagePlus from a VoxelsUntyped.
from(Channel) - Static method in class ConvertToImagePlus: Creates an ImagePlus from a Channel.
from(Stack, boolean) - Static method in class ConvertToImagePlus: Creates an ImagePlus from a Stack.
from(VoxelsUntyped, int) - Static method in class ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a VoxelsUntyped.
FromAnnotations<T extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.file
FromAnnotations() - Constructor for class FromAnnotations
FromByte - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned byte.
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class ConvertToImg: Creates an Img from a VoxelBuffer with an unsigned byte data-type.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class ConvertToImg: Creates an Img from Voxels with an unsigned byte data-type.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class ConvertToNativeImg: Creates an NativeImg from Voxels with an unsigned byte data-type.
fromByte(SliceBufferIndex<UnsignedByteBuffer>, int) - Static method in class ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedByteBuffer.
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type ByteBuffer) that is already a slice.
FromChannel - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Creates image-dimensions by referencing them from a ChannelProvider.
FromChannel() - Constructor for class FromChannel
FromChannel - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
FromChannel() - Constructor for class FromChannel
FromChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as off, and 255 values as on.
FromChannel() - Constructor for class FromChannel
FromChannelBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Base-class for MaskProviders that accept a Channel as input.
FromChannelBase() - Constructor for class FromChannelBase
FromChannelOrMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Creates a stack from a channel or mask (reusing the voxel buffers)
FromChannelOrMask(ChannelProvider) - Constructor for class FromChannelOrMask
FromChannelOrMask() - Constructor for class FromChannelOrMask
FromCSVInput - Class in org.anchoranalysis.plugin.mpp.experiment.objects
FromCSVInput(MultiInput, Path) - Constructor for class FromCSVInput
FromCSVInputManager - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
FromCSVInputManager() - Constructor for class FromCSVInputManager
FromCSVSharedState - Class in org.anchoranalysis.plugin.mpp.experiment.objects: Shared-state for ExportObjectsFromCSV
FromCSVSharedState() - Constructor for class FromCSVSharedState
FromDescriptiveName - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix.
FromDescriptiveName() - Constructor for class FromDescriptiveName
FromDictionary<T extends FeatureInputDictionary> - Class in org.anchoranalysis.plugin.operator.feature.bean: Extracts a key-value from a Dictionary as a double.
FromDictionary() - Constructor for class FromDictionary
FromDictionaryBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
FromDictionaryBase() - Constructor for class FromDictionaryBase
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
FromDimensionsBase() - Constructor for class FromDimensionsBase
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider
FromDimensionsBase() - Constructor for class FromDimensionsBase
FromDimensionsBase<T extends FeatureInputDimensions> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Base class for features that are calculated from Dimensions.
FromDimensionsBase() - Constructor for class FromDimensionsBase
FromDualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
FromDualVoxelizedMarks() - Constructor for class FromDualVoxelizedMarks
FromEntries - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromEntries() - Constructor for class FromEntries
fromFiles(Collection<File>) - Static method in class CommonPath: Finds the common root directory of the paths to several Files.
FromFiles - Class in org.anchoranalysis.io.input.bean.path.provider: Extracts a path from a FilesProvider.
FromFiles() - Constructor for class FromFiles
FromFloat - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type float.
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class ConvertToImg: Creates an Img from a VoxelBuffer with a float data-type.
fromFloat(Voxels<FloatBuffer>) - Static method in class ConvertToImg: Creates an Img from Voxels with a float data-type.
fromFloat(Voxels<FloatBuffer>) - Static method in class ConvertToNativeImg: Creates an NativeImg from Voxels with a float data-type.
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type FloatBuffer) that is already a slice.
FromHistogram - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Each input-file describes a histogram that produces one row of features.
FromHistogram() - Constructor for class FromHistogram
FromImage - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Calculates features from a single image.
FromImage() - Constructor for class FromImage
FromImageMetadata - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Calculates features from the metadata from single image.
FromImageMetadata() - Constructor for class FromImageMetadata
FromInput - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Finds the input-stack using a conventional name of input_image - and extracts the first channel
FromInput() - Constructor for class FromInput
FromInput - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Finds the input-stack using a conventional name of input_image
FromInput() - Constructor for class FromInput
FromInt - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned int.
fromIterable(Iterable<Feature<T>>) - Static method in class FeatureListFactory: Creates a list of features from an iterable
FromList - Class in org.anchoranalysis.bean.shared.color.scheme: Specifies a list of colors by a list.
FromList() - Constructor for class FromList
FromMarkProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromMarkProposer() - Constructor for class FromMarkProposer
FromMarks - Class in org.anchoranalysis.plugin.mpp.bean.object.provider: Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.
FromMarks() - Constructor for class FromMarks
FromMask - Class in org.anchoranalysis.overlay.object.scaled
FromMask() - Constructor for class FromMask
FromMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
FromMask() - Constructor for class FromMask
FromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Converts a binary-mask to an object-collection (containing a single object)
FromMask() - Constructor for class FromMask
FromMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
FromMaskBase() - Constructor for class FromMaskBase
FromMetadata - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromMetadata() - Constructor for class FromMetadata
fromObject(ObjectMask) - Static method in class ConvertToMat: Convert a ObjectMask to a Mat.
FromObjects - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a Mask from a collection of object-masks.
FromObjects() - Constructor for class FromObjects
FromObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromObjects() - Constructor for class FromObjects
FromObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.source: Extracts features for each object in a collection.
FromObjects() - Constructor for class FromObjects
FromOutputName - Class in org.anchoranalysis.plugin.io.bean.file.namer
FromOutputName() - Constructor for class FromOutputName
fromPath(Path) - Static method in class ImageFileAttributes: Reads ImageFileAttributes from a path.
fromPath(Path) - Static method in class ImageTimestampsAttributesFactory: Reads ImageTimestampsAttributes from a path, trying to infer the acquisition-date from metadata headers.
fromPaths(Iterable<Path>) - Static method in class CommonPath: Finds the common root directory of several Paths.
fromPhysicalArea(double) - Method in class UnitConverter: Converts from physical-area to pixels.
fromPhysicalArea(double, String) - Method in class UnitConverter: Converts from physical-area to pixels.
fromPhysicalDistance(double, DirectionVector) - Method in class UnitConverter: Converts from physical-distance to voxels.
fromPhysicalDistance(double) - Method in class UnitConverter: Converts from physical-distance to voxels.
fromPhysicalVolume(double) - Method in class UnitConverter: Converts from physical-volume to voxels.
fromPhysicalVolume(double, String) - Method in class UnitConverter: Converts from physical-volume to voxels.
fromProvider(Provider<Feature<T>>) - Static method in class FeatureListFactory: Creates a list for a single-feature created from a provider
FromProvider - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromProvider() - Constructor for class FromProvider
fromProviders(Collection<FeatureProvider<T>>) - Static method in class FeatureListFactory: Creates a list of features from a collection of feature-providers
fromRepeated(int, Supplier<ObjectMask>) - Static method in class ObjectCollectionFactory: Creates a new collection by repeatedly calling a function to create a single ObjectMask.
FromSerializedMarks - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromSerializedMarks() - Constructor for class FromSerializedMarks
FromSerializedObject - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
FromSerializedObject() - Constructor for class FromSerializedObject
fromSet(Set<ObjectMask>) - Static method in class ObjectCollectionFactory: Creates a new collection from a set of ObjectMask.
FromShort - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned short.
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class ConvertToImg: Creates an Img from a VoxelBuffer with an unsigned short data-type.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class ConvertToImg: Creates an Img from Voxels with an unsigned short data-type.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class ConvertToNativeImg: Creates an NativeImg from Voxels with an unsigned short data-type.
fromShort(SliceBufferIndex<UnsignedShortBuffer>, int) - Static method in class ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedShortBuffer.
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type ShortBuffer) that is already a slice.
FromSingle - Class in org.anchoranalysis.bean.shared.color.scheme: A single color repeated to meet the size.
FromSingle() - Constructor for class FromSingle
FromSingleMark - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
FromSingleMark() - Constructor for class FromSingleMark
fromSlice(VoxelsUntyped, int) - Static method in class ConvertToImg: Creates an Img from a single z-slice of a VoxelsUntyped.
fromSlice(Voxels<UnsignedByteBuffer>, int, String) - Static method in class ConvertToImagePlus: Creates an ImagePlus from one slice of a Voxels<UnsignedByteBuffer> voxels.
FromStack - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Extracts a channel from a provider of a stack
FromStack(ProviderAsStack) - Constructor for class FromStack
FromStack() - Constructor for class FromStack
fromStack(Stack) - Static method in class ConvertToMat: Converts a Stack to a Mat.
FromStackChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
FromStackChannel() - Constructor for class FromStackChannel
FromStackReader - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: Uses a StackReader to read the image-metadata.
FromStackReader() - Constructor for class FromStackReader
FromStacks - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a a subset of channels from a set of stacks
FromStacks() - Constructor for class FromStacks
fromStream(Stream<Feature<T>>) - Static method in class FeatureListFactory: Creates a list of features from a stream
fromStream(Stream<Point3i>) - Static method in class BoundingBoxFromPoints: Create from a stream of Point3is.
fromStrings(Collection<String>) - Static method in class CommonPath: Finds the common root directory of several paths, encoded in Strings.
fromTwoPoints(Point3d, Point3d) - Static method in class BoundingBoxFromPoints: Creates a bounding-box for two unordered points.
FromUnitValueDistance - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
FromUnitValueDistance() - Constructor for class FromUnitValueDistance
fromVoxelBufferByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class ConvertToMat: Converts a VoxelBuffer of type UnsignedByteBuffer to a Mat.
fromVoxelBufferFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class ConvertToMat: Converts a VoxelBuffer of type FloatBuffer to a Mat.
fromVoxelBufferShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class ConvertToMat: Converts a VoxelBuffer of type UnsignedShortBuffer to a Mat.
FromVoxelizedMarksWithEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
FromVoxelizedMarksWithEnergy() - Constructor for class FromVoxelizedMarksWithEnergy
fromVoxelsByte(Voxels<UnsignedByteBuffer>) - Static method in class ConvertToMat: Converts a Voxels of type UnsignedByteBuffer to a Mat.
fromVoxelsFloat(Voxels<FloatBuffer>) - Static method in class ConvertToMat: Converts a Voxels of type FloatBuffer to a Mat.
fromVoxelsShort(Voxels<UnsignedShortBuffer>) - Static method in class ConvertToMat: Converts a Voxels of type UnsignedShortBuffer to a Mat.
FromXMLList - Class in org.anchoranalysis.bean.define.adder: Adds a list of Named-Items define in a XML file in the current directory.
FromXMLList() - Constructor for class FromXMLList
function(String) - Static method in class DescriptionMatch
FunctionalIterate - Class in org.anchoranalysis.core.functional: Utilities for repeating operations a certain number of times.
FunctionalList - Class in org.anchoranalysis.core.functional: Utility functions for manipulating or creating List in a functional way.
FunctionalProgress - Class in org.anchoranalysis.core.functional: Utilities for updating a Progress in a functional way.
functionAndType(String, String) - Static method in class DescriptionMatch

G

GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
GaussianBlur2D() - Constructor for class GaussianBlur2D
GaussianCumulative<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
GaussianCumulative() - Constructor for class GaussianCumulative
GaussianSampler - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar: Samples from a Gaussian distribution whose parameters are determined by a Dictionary.
GaussianSampler() - Constructor for class GaussianSampler
generalWriteException(Class<T>, Path, Exception) - Static method in class WriterErrorMessageHelper: Creates a ImageIOException with an error message that image-writing failed.
generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawCroppedObjectsGenerator
generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawObjectsGenerator
generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface AddCriteria
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaEnergyPair
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaNever
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
generateIntersectingObjects(int, int, boolean) - Static method in class IntersectingCircleObjectsFixture: Generates a number of circles that intersect and don't intersect
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
generateMasks(ObjectCollectionWithProperties) - Method in class DrawCroppedObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class DrawObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class ObjectsAsRGBGenerator
generateNormal(double, double) - Method in interface RandomNumberGenerator: Generates a Gaussian (Normal) random variable with particular parameterization.
generateNormal(double, double) - Method in class RandomNumberGeneratorMersenne
generatePoisson(double) - Method in interface RandomNumberGenerator: Generates a Poisson random variable with particular parameterization.
generatePoisson(double) - Method in class RandomNumberGeneratorMersenne
generateProperties(Optional<Resolution>) - Method in class Ellipse
generateProperties(Optional<Resolution>) - Method in class Ellipsoid
generateProperties(Optional<Resolution>) - Method in class Mark
generateProperties(Optional<Resolution>) - Method in class MarkWithPosition
generateProperties(Optional<Resolution>) - Method in class OverlayMark
generateProperties(Optional<Resolution>) - Method in class OverlayObjectMask
generateProperties(Optional<Resolution>) - Method in class Overlay
GenerateString - Class in org.anchoranalysis.image.io.bean.stack.combine
GenerateString(String) - Constructor for class GenerateString
GenerateString() - Constructor for class GenerateString
GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider: Generates colors to match the size of an object-collection.
GenerateToMatchObjects() - Constructor for class GenerateToMatchObjects
GenerateUniqueParameterization - Interface in org.anchoranalysis.bean: Objects that must implement well-defined equals() and hashCode() methods and also generate a name uniquely identifying the class and all parameterization.
generator() - Static method in class ObjectCollectionWriter
Generator<T> - Interface in org.anchoranalysis.io.generator: A class that writes a particular type of object(s) to the filesystem.
GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator: Exposes a Generator<T> as if it was an Generator<S>.
GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator: Settings and methods for writing to the filesystem from a generator.
Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
Geometry() - Constructor for class Geometry
Geometry(double, double) - Constructor for class Geometry
get() - Method in interface Provider: Gets or creates an object of type T.
get() - Method in class DictionaryProviderReference
get() - Method in class CachedSupplier
get(K) - Method in class LRUCache: Get a value, calculating if necessary, and caching the result.
get(int) - Method in interface ColorIndex: The color for a particular index.
get(int) - Method in class ColorIndexModulo
get(int) - Method in class ColorList
get(int) - Method in class SingleColor
get() - Method in interface CheckedSupplier: Applies a supplier like with Supplier.get().
get() - Method in interface StoreSupplier: Gets the object being supplied to the store.
get(Progress) - Method in class CachedProgressingSupplier
get(Progress) - Method in interface CheckedProgressingSupplier: Applies a supplier like with Supplier.get().
get() - Static method in class ProgressIgnore: Gets a singleton instance of the class.
get() - Method in class Define
get() - Method in class DefinedNamed
get() - Method in class DefineSingle
get(int) - Method in class FeatureList: Returns the element at the specified position in this list.
get() - Method in class PrependName
get() - Method in class FeatureProviderDefine
get() - Method in class FeatureProviderReference
get() - Method in interface FeatureCalculationInput: The underlying feature-input.
get(int) - Method in class LabelledResultsVector: The result of a feature-calculation stored at a particular index.
get(int) - Method in class FeatureNameList: Gets a name corresponding to a particular position.
get(int) - Method in class ResultsVector: The result of a feature-calculation stored at a particular index.
get(int) - Method in class ResultsVectorList: Gets a ResultsVector at a particular position i nthe list.
get() - Method in interface CacheSupplier
get() - Method in class SessionInputSequential
get(int) - Method in class NamedFeatureStore: Gets a feature at a particular position.
get(String) - Method in class NamedFeatureStore: Gets a feature corresponding to a particular name.
get(int) - Method in class BoundingBoxesOnPlane
get(int, int) - Method in class TableItemArrangement
get() - Method in class ChannelProviderBinary
get() - Method in class ChannelProviderTernary
get() - Method in class ChannelProviderUnary
get() - Method in class HistogramProviderUnary
get() - Method in class MaskProviderUnary
get() - Method in class ObjectCollectionProviderUnary
get() - Method in class ArrangeRaster
get() - Method in class StackProviderUnary
get(int) - Method in class ObjectCollectionWithProperties: Get an item at a particular index.
get(Progress) - Method in interface NamedStacksSupplier: Gets the NamedProvider of Stacks.
get() - Method in class GenerateString
get() - Method in class TileWithLabels
get(String) - Method in class NamedEntries
get(Progress) - Method in interface TimeSequenceSupplier
get(int) - Method in class StackSeries
get(int) - Method in class TimeSequence
get(VoxelDataType) - Method in class VoxelDataTypeFactoryMultiplexer: Multiplexes one of the factories according to data-type
get(int) - Method in class ObjectCollection: Get an ObjectMask at a particular position in the collection.
get(int) - Method in interface DestinationChannelForIndex
get() - Method in class ReadFromFile
get() - Method in class FilePathProviderReference
get() - Method in class FromFiles
get() - Method in interface PathSupplier
get(int) - Method in class DeriveElementsFromSequencedDirectory
get(int) - Method in interface SupplierAtIndex
get() - Method in class FinderDictionary
get() - Method in class FinderFileAsText
get() - Method in class FinderSerializedObject
get() - Method in interface SerializedObjectSupplier
get(Optional<String>) - Method in class InputOutputContextSubdirectoryCache: Gets (from the cache if it's already there) a context for a subdirectory of given-name
get() - Method in interface ElementSupplier: Gets/creates the element to be written.
get() - Method in interface ElementWriterSupplier: Gets/creates the ElementWriter to be used for an output.
get(int) - Method in class RunningSumCollection: An individual item in the collection.
get(int) - Method in class ImageMoments: Get an eigenvalue and corresponding eigenvector for a particular axis.
get(int) - Method in class MarksWithTotalEnergy
get(int) - Method in class EnergySavedInd
get(String) - Method in class EnergySchemeSet
get(int) - Method in class MemoList
get(int) - Method in class UpdatableMarksList
get(int) - Method in class IndexByChannel
get(String) - Method in interface MultiInputSubMap: Returns null if non-existent
get(String) - Method in class OperationMap
get(String) - Method in class StackWithMap
get(int) - Method in class MarkCollection
get(int) - Method in class AggIDCounter
get(int) - Method in class WeightedKernelList
get(int) - Method in class ColoredOverlayCollection
get(int) - Method in class OverlayCollection
get(T, int) - Method in interface GetForSeries
get(String) - Method in class GroupedAnnotationLabels
get() - Method in class FromDimensionsBase
get() - Method in class FromInput
get() - Method in class FromStack
get() - Method in class FromMaskBase
get() - Method in class Reference
get() - Method in class ScoreVoxels
get() - Method in class Concatenate
get() - Method in class GenerateToMatchObjects
get() - Method in class FromChannel
get() - Method in class GuessDimensions
get() - Method in class SpecifyDimensions
get() - Method in class FromChannel
get() - Method in class Reference
get() - Method in class FromStackChannel
get() - Method in class FromChannelBase
get() - Method in class FromDimensionsBase
get() - Method in class Reference
get() - Method in class Concatenate
get() - Method in class ConnectedComponentsFromMask
get() - Method in class Empty
get() - Method in class IfParamEqual
get() - Method in class FromMask
get() - Method in class MergeTwoCollectionsItemwise
get() - Method in class Permute
get() - Method in class Reference
get() - Method in class ReferenceOrElse
get() - Method in class SegmentStack
get() - Method in class WithChannelBase
get() - Method in class ColoredBase
get() - Method in class ThreeChannels
get() - Method in class Concatenate
get() - Method in class FromChannelOrMask
get() - Method in class FromInput
get() - Method in class PlotHistogram
get() - Method in class Reference
get() - Method in class IntensityMoments
get() - Method in class DeriveFromPair
get() - Method in class FeatureListProviderAggregatePair
get() - Method in class PermuteFeatureBase
get(int) - Method in class ListWithThumbnails
get() - Method in class PriorityQueueIndexRangeDownhill
get(T) - Method in class FileLabelMap
get() - Method in class DeserializedManifest
get() - Method in class FeatureListProviderLDAClassifier
get() - Method in class FeatureListProviderSVMClassifier
get() - Method in class MarkBoundsDefine
get() - Method in class MarkBoundsReference
get() - Method in class FromMarks
get() - Method in class CreateNew
get() - Method in class FromSingleMark
get() - Method in class PointsFromObjects
get() - Method in class Reference
get() - Method in class ReferenceOrEmpty
get() - Method in class ScaleXY
get() - Method in class CreateEllipse
get() - Method in class RequireFeatureRelationThreshold
get() - Method in class RetrieveSingleMarkOnly
get(int) - Method in class ContiguousVoxelPath
get(String) - Method in class IndexedCSVRows
get(String) - Method in class MapGroupToRow
get() - Method in class HOGDescriptor
get() - Method in interface FeatureResultSupplier
get() - Method in class FitPointsFromObjects
get(int) - Method in class BoundedList: Gets a particular element.
getAboveMaxValue() - Method in class RangeCompareBase: Constant to return if outside the range (above the maximum allowed)
getAcceptAll() - Method in class Aggregator
getAcqusitionTime() - Method in class ImageMetadata: A timestamp, if available, of when the image was first physically created by the camera/device.
getAcqusitionTime() - Method in class ImageTimestampsAttributes: A timestamp, if available, of when the image was first physically created by the camera/device.
getAdd() - Method in class VisualizeOnBackground
getAddCriteria() - Method in class RandomCollectionWithAddCriteria
getAdditionalBackgrounds() - Method in class MarkProposerStrategy: Additional background-stacks that are possible to use while annotating.
getAdditionalChannels() - Method in class MultiInputManagerQuick: Additional channels other than the main one, which are located in the main raster file
getAdditionalChannels() - Method in class NamedChannelsQuick: Additional channels other than the main one, which are located in the main raster file
getAdditionalPropertyPaths() - Method in class PermuteProperty: Additional property paths that are also changed, together with propertyPath.
getAddSum() - Method in class GradientBaseAddSum: Added to all gradients (so we can store negative gradients)
getAdjacentChannels() - Method in class NamedChannelsQuick: Channels that are located in a separate raster file adjacent to the main raster file
getAfterPreoperation() - Method in class OverlappingObject: After pre-operation but before scaling
getAggInterval() - Method in class ReporterInterval
getAggIntervalLog10() - Method in class ReporterInterval: How many iterations before printing a new report? Encoded in log10.
getAggregateReceiver() - Method in class ReporterAggregate
getAggregateReceiver() - Method in class ConsoleAggregatedReporter
getAggregateReceiver() - Method in class CSVReporterAggregated
getAggregateReceiver() - Method in class Log4JReporter
getAggregateReceiver() - Method in class MemoryUsageReporter
getAggregateReceiver() - Method in class OptimizationStepLogReporter
getAggregateReceiver() - Method in class TextFile
getAggregateTriggerBank() - Method in class FeedbackBeginParameters
getAll() - Method in class MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
getAllCacheNames() - Method in class CacheTransferSourceCollection
getAllKernelFactories() - Method in class KernelProposer
getAllowsChildren() - Method in class ErrorNodeImpl
getAngle() - Method in class OrientationAxisAngle: Angle part of axis-angle orientation (anti-clock in radians).
getAngleDegrees() - Method in class Orientation2D: The angle of the rotation in the 2D plane anti-clockwise, in degrees.
getAnnealScheme() - Method in class SimulatedAnnealing
getAnnotations() - Method in class FromAnnotations
getAnnotatorStrategy() - Method in class AnnotationInputManager: The strategy to be used for annotating.
getAppendChannels() - Method in class NamedChannelsQuick: Channels that are located in a separate raster file somewhere else in the project's structure
getAppendCSV() - Method in class FromCSVInputManager
getAppendCsv() - Method in class MatchedAppendCsv
getAppendDictionary() - Method in class MultiInputManager
getAppendFilePath() - Method in class MultiInputManager
getAppendHistogram() - Method in class MultiInputManager
getAppendMarks() - Method in class MultiInputManager
getAppendMarksFromAnnotation() - Method in class MultiInputManager
getAppendMarksFromAnnotationAcceptedOnly() - Method in class MultiInputManager
getAppendMarksFromAnnotationRejectedOnly() - Method in class MultiInputManager
getAppendObjects() - Method in class MultiInputManager: Appends object-collections to the MultiInput.
getAppendStack() - Method in class MultiInputManager
getArbitraryElement() - Method in interface NamedProvider: Gets one element of the provider (arbitrarily).
getArrange() - Method in class ArrangeRaster
getArrange() - Method in class Cell
getArrange() - Method in class CombineRasterGenerator
getAsBoolean() - Method in interface CheckedBooleanSupplier: Applies a supplier like with BooleanSupplier.getAsBoolean().
getAsDouble(String) - Method in class Dictionary: Retrieves a value from the dictionary, and converts to a double.
getAssigner() - Method in class CompareAnnotations
getAssignmentCSV() - Method in class ComparisonSharedState
getAssignMode() - Method in class SimulatedAnnealing
getAssociatedElementRange() - Method in class MutableDirectory
getAssociatedElementRange() - Method in interface SequencedDirectory: The associated element-range with ths folder.
getAssociatedMark() - Method in class ErrorNodeImpl
getAsStack() - Method in class ChannelProvider
getAsStack() - Method in class MaskProvider
getAsStack() - Method in class StackProvider
getAsStack() - Method in interface ProviderAsStack: Retrieves or creates a Stack representation of an entity.
getAsString(String) - Method in class Dictionary: Retrieves a value from the dictionary as a String.
getAttributes() - Method in class ImageTimestampsAttributes: Timestamps and other metadata associated with an image file-path, but not with the file's contents.
getAttributes() - Method in class StackWriteOptions: The attributes of the particular stack to write.
getAxis() - Method in class AxisAlignedUnitVector: Which axis the unit-vector will align with.
getAxis() - Method in class CenterOfGravity
getAxis() - Method in class GradientForAxis: Which axis? X=0, Y=1, Z=2
getAxis() - Method in class ForSpecificAxis
getAxis() - Method in class ArbitraryInsidePoint
getAxis() - Method in class BoundingBoxAlongAxisBase
getAxis() - Method in class GradientMeanForAxis
getAxis() - Method in class PrincipalAxisOrientation: Which axis to read from (x,y,z)
getAxis() - Method in class BoundingBoxExtent
getAxis() - Method in class OrientationAxisAngle: Axis part of axis-angle orientation (should be normalized).
getAxisColor() - Method in class PlotColorScheme
getAxisMax() - Method in class AxisLimits
getAxisMin() - Method in class AxisLimits
getBackground() - Method in class AnnotatorStrategy: The visual background to use while annotating.
getBackground() - Method in class ObjectsAsRGBGenerator: A background image or dimensions to define an empty background.
getBackground() - Method in class DualStack: The background
getBackground() - Method in class CompareAnnotations: The name of the stack to use as background to the annotations.
getBackground() - Method in class ColoredBase: The background.
getBackgroundChannelIndex() - Method in class OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
getBackgroundChannelProvider() - Method in class MorphologicalOperatorBase
getBackgroundColor() - Method in class PlotColorScheme
getBackgroundID() - Method in class VisualizeOnBackground
getBackgroundStackMap() - Method in class AnnotationBackground: If non-null, maps underlying stack-name to a background.
getBackgroundStackName() - Method in class SegmentIntoMarks
getBaseName() - Method in class FilenameSplitExtension: The part of the filename without an extension.
getBeanExtension() - Method in class QuickMultiDatasetExperiment
getBeanExtension() - Method in class QuickMultiDatasetStructuredExperiment
getBeanName() - Method in class AnchorBean: A short-name identifying a bean (by default the name of the class associated with the bean).
getBelowMinValue() - Method in class RangeCompareBase: Constant to return if outside the range (below the minimum allowed)
getBest() - Method in class DualState
getBest() - Method in class OptimizationStep
getBestState() - Method in class Reporting
getBinaryInputChannelID() - Method in class AddDistanceTransform: The ID of the binary input mask that determines the region of the Watershed.
getBinarySgmn() - Method in class BinarySegmentByObject
getBirthRepeats() - Method in class KernelReplace
getBitDepthPerChannel() - Method in class ImageMetadata: The number of bits in memory to describe each voxel's intensity, per channel.
getBitsPerPixel() - Method in class ForceBitsPerPixel
getBlockSize() - Method in class HOGParameters: The block-size as per OpenCV implementation (identical default-size).
getBlockStride() - Method in class HOGParameters: The block-stride as per OpenCV implementation (identical default-size).
getBlue() - Method in class RGBColorBean: The blue component value of the RGB color.
getBlue() - Method in class RGBColor: The blue component value of the RGB color.
getBlue() - Method in class ThreeChannels
getBorderWidth() - Method in class MontageSlices: Adds a border around each part of the montage
getBoundRadius() - Method in class MarkWithPositionAndSingleRadius
getBounds() - Method in class RandomOrientation
getBridgeMatcher() - Method in class Bridge: Used to match each input-object to an intermediary-object
getBundleSize() - Method in class ObjectSerializerPeriodicReporter
getBundleSize() - Method in class VoxelizedMarksChangeReporter
getCache() - Method in interface FeatureCalculationInput: Get the associated FeatureCalculationCache.
getCache() - Method in class CacheAndReuseStrategy
getCache() - Method in class SessionInputSequential
getCacheNames() - Method in class CacheTransferSource
getCacheSize() - Method in class RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
getCalculateLevel() - Method in class CalculateLevelOne
getCalculateLevel() - Method in class ThresholderGlobal
getCalculateLevel() - Method in class LevelPerObjectBase: Method to calculate the level for a particular object.
getCalculateLevel() - Method in class GreaterThanThreshold: Calculates the level for the threshold
getCalculateLevel() - Method in class LevelFromHistogram
getCalculateLevel() - Method in class ThresholdHistogram
getCalculateLevel() - Method in class CalculateLevelBase
getCalculateLevelElse() - Method in class CalculateLevelRelativeToThreshold
getCalculator() - Method in class NamedFeatureCalculatorMulti
getCellDefault() - Method in class Tile
getCells() - Method in class Tile
getCellSize() - Method in class HOGParameters: The cell-size as per OpenCV implementation (identical default-size).
getCenter() - Method in class SlidingBuffer: The buffer for the currently selected slice.
getCenterPoint() - Method in class FitResult
getCenterPointX() - Method in class EllipseStandardFormConverter
getCenterPointY() - Method in class EllipseStandardFormConverter
getChangedMarkIDArr() - Method in class KernelDecision
getChangedMarkIDs() - Method in class Reporting
getChannel(int) - Method in class EnergyStack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class EnergyStackWithoutParameters: Returns the channel at a particular position in the stack.
getChannel() - Method in class ChannelProviderUnary
getChannel(int) - Method in class RGBStack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class Stack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class StackNotUniformSized: Returns the channel at a particular position in the stack.
getChannel(String, int, Progress, Logger) - Method in class ChannelFilter
getChannel() - Method in class ChannelFilter
getChannel(String, int, Progress, Logger) - Method in interface ChannelGetter
getChannel(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
getChannel(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
getChannel() - Method in class FromChannel: The ChannelProvider to use for dimensions.
getChannel() - Method in class FromChannel
getChannel() - Method in class FromChannelBase
getChannel() - Method in class IntensityGreaterEqualThan
getChannel() - Method in class UnaryWithChannelBase
getChannel() - Method in class WithChannelBase
getChannel() - Method in class FromChannelOrMask: A channel that is provided to the stack.
getChannel() - Method in class NamedChannel
getChannel(String, Logger) - Method in class ChannelGetterForTimepoint
getChannel1() - Method in class ChannelProviderBinary
getChannel1() - Method in class ChannelProviderTernary
getChannel2() - Method in class ChannelProviderBinary
getChannel2() - Method in class ChannelProviderTernary
getChannel3() - Method in class ChannelProviderTernary
getChannelAssignFrom() - Method in class AssignFromChannel
getChannelChecker() - Method in class GroupedSharedState
getChannelConversionStyle() - Method in class ConvertImageFormat: To convert as RGB or independently or in another way.
getChannelConverter() - Method in class Convert
getChannelConverter() - Method in class ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
getChannelElse() - Method in class IfParamEquals
getChannelFilter() - Method in class ConvertImageFormat: Optionally, includes only certain channels when converting.
getChannelFirst() - Method in class Difference: Index of first channel
getChannelGroupID() - Method in class RegularExpression
getChannelID() - Method in class AddEdgeFilters: The ID of the channel that provides the input to the filter
getChannelIfVoxelZero() - Method in class IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
getChannelIndex() - Method in class FromStack
getChannelIndex() - Method in class FromStackChannel
getChannelIndex() - Method in class One
getChannelIndex() - Method in class FileDetails
getChannelIndex() - Method in class MultiInputManagerQuick: If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
getChannelLookup() - Method in class NormalizeDifferenceToMedian
getChannelMap() - Method in class NamedChannels
getChannelMask() - Method in class ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
getChannelName() - Method in class ChannelFilter
getChannelName() - Method in class SingleChannel
getChannelName() - Method in class ConvertNamedChannelsToStack: By default all channels are converted into a stack.
getChannelNum() - Method in class SortedSetChannel
getChannelOptional(String, int, Progress, Logger) - Method in interface NamedChannelsForSeries: Gets a channel if it exists, returning empty if it doesn't.
getChannelOptional(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
getChannelOptional(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
getChannelSecond() - Method in class Difference: Index of second channel
getChannelsExtra() - Method in class ScoreVoxels
getChannelsPerByteArray() - Method in class ForceChannelsPerByteArray
getChannelThreshold() - Method in class ThresholdAgainstChannel
getChannelType() - Method in class ConsistentChannelChecker
getChart() - Method in class PlotInstance
getCheck() - Method in class Not
getChecked() - Method in class Outputter: Gets the underlying delegate of Outputter that throws checked-exceptions instead of using a ErrorReporter.
getCheckMark() - Method in class FromObjects
getCheckMark() - Method in class Check
getCheckMark() - Method in class Check
getCheckParsedFilePathBag() - Method in class GroupFiles: Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.
getChildAt(int) - Method in class ErrorNodeImpl
getChildCount() - Method in class ErrorNodeImpl
getClassifierProvider() - Method in class BinaryClassifierImageLabeller
getCode(int) - Method in class EncodedIntBuffer
getCol(int) - Method in class TableItemArrangement
getCol() - Method in class Cell
getColForListIndex(int) - Method in class TableItemArrangement
getCollection() - Method in class KernelDeath.MarkAnd
getColor() - Method in class FromSingle: The single color to repeat.
getColor(int) - Method in class ColoredOverlayCollection
getColor() - Method in class AnnotationLabel: An optional color associated with the label when displayed via GUI
getColor() - Method in class ColoredMask
getColorIDGetter() - Method in class ObjectDrawAttributes: Gets a color ID associated with the object
getColorIndex() - Method in class ObjectDrawAttributes: Colors for a given index
getColorList() - Method in class ColoredMarks
getColors() - Method in class ColorSchemeUnary: The delegate that creates the color-list before subsequent processing.
getColors() - Method in class FromList: The list of colors to specify.
getColors() - Method in class ColoredOverlayCollection
getColors() - Method in class ColoredBaseWithGenerator: Colors to use for drawing objects
getColors() - Method in class ColoredObjectCollection: The colors in the collection.
getColorScheme() - Method in class GenerateToMatchObjects
getColorsUnpaired() - Method in class CompareAnnotations
getColorUnselectedObjects() - Method in class OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
getColumnDefinition() - Method in class ExportObjectsFromCSV: Column definition for the CSV files
getColumnGroup() - Method in class ColumnDefinition: Name of CSV column used to group results (the same values, are outputted together)
getColumnID() - Method in class ColumnDefinition: Name of CSV column with the file identifier
getColumns() - Method in class MontageSlices: How many columns to use in the montage, or 0 to guess an approximately square output
getColumnUniquePixel() - Method in class ColumnDefinition: Name of CSV column with X coordinate of point for the first Object
getCombine() - Method in class FromObjects
getCombined() - Method in interface VoxelPartition
getCombined() - Method in class VoxelPartitionHistogram
getCommand() - Method in class MorphologicalOperation: One of: open, close, fill, erode, dilate, skel, outline
getCommandName() - Method in class HelpConfig: What the application command is described as in the help message e.g. anchor or anchorGUI
getComparerLeft() - Method in class AnnotationComparisonInputManager
getComparerMultiplex(boolean) - Method in class AnnotationComparisonInput
getComparerRight() - Method in class AnnotationComparisonInputManager
getComparers() - Method in class AnnotationComparisonInput
getCondition() - Method in class IfParamEquals
getCondition() - Method in class IfKeyValueCondition
getConnPoint() - Method in class ContiguousVoxelPath
getConstant() - Method in class MaxWithConstant
getContains() - Method in class DescriptiveNameContainsImageLabeller
getContains() - Method in class FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
getContext() - Method in class SharedObjects: Logger and other common configuration
getContext() - Method in class ParametersExperiment
getContext() - Method in class OutputterChecked: General settings for writing outputs.
getContext() - Method in class FeatureCalculationContext
getContext() - Method in class FeatureExporterContext: Context for reading from or writing outputs to the file-system.
getContextExperiment() - Method in class InputBound: The input-output context associated with the current experiment.
getContextJob() - Method in class InputBound: The input-output context associated with the current job.
getConversion() - Method in class ConvertedInput: The converted input.
getConvert() - Method in class ConvertWithHistogram
getConverters() - Method in class DisplayStack: A list of optional converters that will be applied to the respective channel in stack if they exist.
getCopyFilesNaming() - Method in class CopyFilesNamingOne
getCost(int, int) - Method in class CostMatrix: Gets the cost from an element from the first-list to an element from the second-list.
getCost() - Method in class MergeStrategy: A cost of how undesirable (the higher the more undesirable) this merge is.
getCosts() - Method in class AssignOverlappingObjects: A matrix linking the overlap between each ObjectMask to each other, respectively as rows and columns.
getCount() - Method in class RecordedExecutionTimes.RecordedOperation: How many times the operation occurred.
getCount() - Method in class Counter: The count, as per current state.
getCount() - Method in class RunningSum: The running count.
getCount(int) - Method in class Histogram: The count corresponding to a particular value.
getCount() - Method in class VarianceCalculatorDouble: The running count of values.
getCount() - Method in class VarianceCalculatorLong: The running count of values.
getCountThreshold() - Method in class SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
getCreateMark() - Method in class PointsFitter
getCreationTime() - Method in class ImageFileAttributes: The creation timestamp on the file the image was loaded from.
getCsvFeaturesAggregated() - Method in class FeatureOutputNames: The CSV of aggregated feature-results, if enabled.
getCsvFeaturesGroup() - Method in class FeatureOutputNames: The CSV individually written for each group, if enabled.
getCsvFeaturesNonAggregated() - Method in class FeatureOutputNames: The CSV of non-aggregated feature-results.
getCsvFilePath() - Method in class FilterCSVColumn
getCsvFilePath() - Method in class FromCSVInput
getCurrent() - Method in class DualState
getCurrent() - Method in class OptimizationStep
getCurrentTemp() - Method in class Geometry
getCustomName() - Method in class Feature: An optional additional name that be associated with the feature (defaults to an empty string).
getDatasetName() - Method in class ExperimentResultsExperimentStructure: The name of the experiment including version suffix
getDatasets() - Method in class QuickMultiDatasetExperiment
getDatasets() - Method in class QuickMultiDatasetStructuredExperiment
getDatasetSpecific() - Method in class QuickMultiDatasetExperiment
getDatasetSpecific() - Method in class QuickMultiDatasetStructuredExperiment
getDatasetSuffix() - Method in class FilePathAppendBase: A suffix appended to the dataset name extracted from the reg exp
getDatasetVersion() - Method in class ExperimentResultsExperimentStructure: A version-suffix appended to the dataset name extracted from the reg exp
getDebugModeParameters() - Method in class InputManagerParameters
getDebugModeParameters() - Method in class InputContextParameters: Parameters for debug-mode (only defined if we are in debug mode)
getDefault() - Static method in class BinaryValuesByte: Default values to use, if not otherwise specified.
getDefault() - Static method in class BinaryValuesInt: Default values to use, if not otherwise specified.
getDefaultBeanClass() - Method in class AnchorDefaultBeanFactory: Returns null as Optional is not supported by BeanFactory interface.
getDefaultColors() - Method in class OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
getDefaultExtension() - Method in interface FileFormat: The default extension to write associated with a particular format.
getDefaultExtension() - Method in enum ImageFileFormat
getDefaultExtension() - Method in enum NonImageFileFormat
getDefaultInstances() - Method in class AnchorDefaultBeanFactory: Default bean-classes to use for particular family types of beans.
getDefaultInstances() - Static method in class RegisterBeanFactories: Default instances of different family-types of beans.
getDefaultStackReaderForMetadata() - Method in class ConvertNamedChannels: Supplies to the imageMetadataReader to use, if no other reader is specified.
getDefine() - Method in class MarkEvaluator
getDefine() - Method in class DefineOutputter
getDefine() - Method in class Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
getDefine() - Method in class ExportReportFeaturesFromMulti
getDefine() - Method in class FromObjects
getDefine() - Method in class ExportObjectsAsCroppedImages
getDefine() - Method in class SegmentWithMarkedPointProcess: Adds definitions of stacks/objects etc.
getDelaySizeAtEnd() - Method in class MovieFromSlices
getDelegate() - Method in class RasterGeneratorDelegateToRaster
getDelegate() - Method in class UnsignedByteBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class UnsignedIntBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class UnsignedShortBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class InputFromManagerDelegate
getDelegate() - Method in class BoundMinMax
getDelegate() - Method in class CalculateInputFromDelegate
getDelimiter() - Method in class SubsetRangeIfRequested: Character used to split the name into groups.
getDelimiter() - Method in class LastDirectoryAsPrefix
getDelta() - Method in class Mser
getDeltat() - Method in class AnisotropicDiffusion: the integration constant for the numerical integration scheme.
getDepth() - Method in class TraversalResult: The depth of directories processed, where 1 = root directory traversed, 2 = root directory + one further level etc.
getDepth() - Method in class ImposeResolution: Physical pixel size of a voxel in z-dimension.
getDerivePath() - Method in class DualMarksAnnotationAsObjects
getDerivePath() - Method in class MarksAsObjects
getDerivePath() - Method in class MaskAsObject: Where to find the Mask to compare, as a function of the source file-path.
getDerivePath() - Method in class Objects: Where to find the objects to compare, as a function of the source file-path.
getDerivePath() - Method in class CollapseFileName
getDerivePath() - Method in class RemoveTrailingDirectory
getDescription() - Method in exception AnchorCombinableException: The (uncombined) description associated with the exception.
getDescription() - Method in class OutputtedFile
getDescription() - Method in class ManifestDirectoryDescription
getDescription() - Method in class KernelDecision
getDescription() - Method in class KernelWithIdentifier
getDestination() - Method in class IdentifiablePair
getDestination() - Method in class PairPxlMarkMemo
getDestination() - Method in class DualVoxelizedMarks
getDestination() - Method in class ToVoxelized
getDestinationDirectory() - Method in class CopyContext: Destination directory for copying.
getDictionaries() - Method in class DictionaryInitialization: Named-store of Dictionary objects.
getDictionary() - Method in class FeatureInitialization: A dictionary of key-value pairs.
getDictionary() - Method in class FeatureRelatedInitialization: A named-mapping to Dictionarys.
getDictionary() - Method in class FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
getDictionary() - Method in class EnergySchemeCreatorByElement
getDictionary() - Method in class ScaleByDictionary
getDictionary() - Method in class AssignFromDictionary: The dictionary from which an assignment will occur.
getDictionary() - Method in class ScoreVoxels
getDictionary() - Method in class DictionaryCondition: The dictionary to provide a value to check.
getDictionary() - Method in class IfParamEqual
getDictionary() - Method in class ParamFromCollection: The name of the Dictionary that will be retrieved from SharedObjects.
getDictionary() - Method in class FeatureListProviderLDAClassifier
getDictionary() - Method in class FeatureValueCheckMark
getDictionary() - Method in class DefineOutputterWithEnergy
getDictionary() - Method in class GaussianSampler: The dictionary that parameterizes the Gaussian-distribution that is sampled from.
getDictionary() - Method in class Develop: If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
getDictionary() - Method in class SegmentMarksFromImage: If non-empty, a dictionary that is passed to the segmentation procedure.
getDictionaryOptional() - Method in interface FeatureInputDictionary: The associated dictionary, if it exists.
getDictionaryOptional() - Method in class FeatureInputEnergy
getDictionaryOptional() - Method in class FeatureInputMark
getDictionaryRequired() - Method in interface FeatureInputDictionary: The associated dictionary, or an exception if it doesn't exist.
getDimensions() - Method in class ImageMetadata: The dimensions of the image.
getDimensions() - Method in class ReportFeatureForMarks
getDimensions() - Method in class FromDimensionsBase
getDimensions() - Method in class FromDimensionsBase
getDimensions() - Method in class RepeatSlice: Dimensions to create new mask
getDimensions() - Method in class MergeBase
getDimensions() - Method in class WithDimensionsBase
getDimensions() - Method in class WithOptionalDimensionsBase
getDimensions() - Method in class ToDimensions: The dimensions the source image/entity is desired to be scaled to.
getDimensions() - Method in class FromMarks
getDimensions() - Method in class RequireFeatureRelationThreshold
getDimensions() - Method in class PointsFitterToMark
getDimensionsOptional() - Method in class FeatureInputMark
getDimensionsRequired() - Method in class FeatureInputMark
getDimensionsSourceFallback() - Method in class ToDimensions: Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getDirection() - Method in class ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis
getDirection() - Method in class FeatureMarkDirection
getDirectionVector() - Method in class LineSegment
getDirectionVector() - Method in class FromUnitValueDistance
getDirectory() - Method in class PathDifference: The directory component of the difference, if it exists.
getDirectory() - Method in class InputArguments: A directory indicating where inputs can be located
getDirectory() - Method in class FilesProviderWithDirectoryString: A directory in which to look for files.
getDirectory() - Method in class FileWithDirectoryInput: A directory that must be a containing directory (at some hierarchical level) of file associated with this input.
getDirectory() - Method in class GlobExtractor.GlobWithDirectory: The directory part of the string, or null if it doesn't exist
getDirectory() - Method in class DualPathPredicates: Only accepts any containing directories where the predicate returns true
getDirectory() - Method in class OutputterTarget
getDirectory() - Method in class DirectoryWithPrefix
getDirectory() - Method in class HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectory
getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectoryString
getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectoryUnary
getDirectoryAsPath(InputContextParameters) - Method in class SingleFile
getDirectoryAsPathEnsureAbsolute(InputContextParameters) - Method in class FilesProviderWithDirectory: Like getDirectory as Path but converts any relative path to absolute one
getDirectoryDataset() - Method in class QuickMultiDatasetExperiment
getDirectoryDistance() - Method in class QuickMultiDatasetStructuredExperiment: How many directories to recurse back from the current file to the Experiments/ directory
getDirectoryOutput() - Method in class QuickExperiment
getDistance() - Method in class LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
getDistance() - Method in class DistanceIndex
getDistance() - Method in class DistanceIndexTwice
getDistanceMapProvider() - Method in class MergeSpatialClusters: A distance map which can also be used for making decisions on merging
getDistanceMax() - Method in class CalculateLevel
getDistanceTransformMultiplyBy() - Method in class AddDistanceTransform: Multiplies the distance transform by this factor to make it more meaningful in a short.
getDistanceTransformSmoothSigmaMeters() - Method in class AddDistanceTransform: If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below.
getDistanceX() - Method in class ReflectInAxesWithinDistance
getDistanceY() - Method in class ReflectInAxesWithinDistance
getDistanceZ() - Method in class ReflectInAxesWithinDistance
getDistanceZEndIfEmpty() - Method in class XYOrientationExtendToZ
getDivideByZeroValue() - Method in class Divide
getDivisor() - Method in class PermutePropertySequenceDouble: What to divide the integer-sequence by.
getDrawObject() - Method in class SimpleOverlayWriter
getDrawObject() - Method in class DrawOverlay
getDscr() - Method in class ResolvedBound
getDualStack() - Method in class OptimizationContext
getEigenvalue() - Method in class EigenvalueAndVector: The eigenvalue.
getEigenvector() - Method in class EigenvalueAndVector: The eigenvector corresponding to eigenvalue.
getElemAllAsFeatureList() - Method in class EnergyScheme
getElemAllCreator() - Method in class EnergySchemeCreatorByElement
getElemByCliqueSize(int) - Method in class EnergyScheme
getElemIndAsFeatureList() - Method in class EnergyScheme
getElemIndCreator() - Method in class EnergySchemeCreatorByElement
getElemPairAsFeatureList() - Method in class EnergyScheme
getElemPairCreator() - Method in class EnergySchemeCreatorByElement
getEllipsoidCalculator() - Method in class Ellipsoid
getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class Ellipsoid
getElseName() - Method in class FileNamerContext: A fallback name, if a failure occurs when naming.
getEmptyValue() - Method in class CenterOfGravity
getEmptyValue() - Method in class Intersection
getEmptyValue() - Method in class ArbitraryInsidePoint
getEmptyValue() - Method in class IntensityMeanMaxSlice
getEmptyValue() - Method in class IntensityMeanShellBase
getEmptyValue() - Method in class DerivedObject
getEnd() - Method in class SequenceInteger: An index beyond which we cannot iterate (inclusive).
getEndIndex() - Method in class IndexRangeNegative: The index if the last element to use in the subsetting range, inclusive.
getEndPoint() - Method in class LineSegment
getEnergy() - Method in class Aggregator
getEnergyChannelIndex() - Method in class Identity
getEnergyChannelIndex() - Method in class RejectIfIntensityLessThan
getEnergyChannelIndex() - Method in class SingleChannel
getEnergyChannelIndex() - Method in class QuantileAcrossConnectedComponents
getEnergyChannelIndexCheck() - Method in class IdentityImposeValueRelationToHistogram
getEnergyChannelIndexFail() - Method in class IdentityImposeValueRelationToHistogram
getEnergyIndex() - Method in class NumberNeighboringVoxels: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class SpecificEnergyChannelBase: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
getEnergyIndex() - Method in class OutsideRange
getEnergyIndex() - Method in class Intensity: The channel that that forms the histogram
getEnergyIndex() - Method in class AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
getEnergyIndex() - Method in class OverlapMaskBase
getEnergyIndexGradient() - Method in class TextureScore
getEnergyIndexMask() - Method in class IntensityMeanShellBase: A channel of the energyStack that is used as an additional mask using default byte values for on and off.
getEnergyIndexMask() - Method in class Intensity: Optionally, index of another channel that masks the histogram.
getEnergyIndexX() - Method in class IntensityGradientBase
getEnergyIndexY() - Method in class IntensityGradientBase
getEnergyIndexZ() - Method in class IntensityGradientBase
getEnergyScheme() - Method in class MarksWithEnergyBreakdown
getEnergyScheme() - Method in class MarksWithTotalEnergy: Associated Energy Scheme, which should include the EnergySavedPairs
getEnergyScheme() - Method in class VoxelizedMarksWithEnergy
getEnergyScheme() - Method in class EnergySchemeWithSharedFeatures
getEnergyScheme() - Method in class KernelCalculationContext
getEnergyScheme() - Method in class OptimizationContext
getEnergySchemeCreator() - Method in class MarkEvaluator
getEnergySchemeCreator() - Method in class SegmentWithMarkedPointProcess: Creates an energy scheme that assigns an energy score to each collection of marks.
getEnergyStack() - Method in class FeatureInitialization: An energy-stack, which may form an input to the feature for calculation.
getEnergyStack() - Method in class ProposerContext
getEnergyStack() - Method in class DualStack: The energy-stack
getEnergyStack() - Method in class FeatureCalculatorFromProvider
getEnergyStack() - Method in class InitializationWithEnergyStack
getEnergyStackOptional() - Method in class FeatureInputEnergy: The associated energy-stack.
getEnergyStackRequired() - Method in class FeatureInputEnergy: The associated energy-stack or throws an exception if it isn't present.
getEnergyTotal() - Method in class EnergyPair
getEnergyTotal() - Method in class MarksWithEnergyBreakdown
getEnergyTotal() - Method in class MarksWithTotalEnergy: The pre-annealed total energy
getEnergyTotal() - Method in class VoxelizedMarksWithEnergy
getEnergyTotal() - Method in class EnergySavedAll
getEnergyTotal() - Method in class EnergySavedInd
getEnergyTotal() - Method in class EnergySavedPairs: Pairwise energy total
getEquals() - Method in class FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
getError(int) - Method in class ResultsVector: Gets an error state at a particular position.
getErrorMessage() - Method in class ErrorNodeImpl
getErrorNode() - Method in class ProposerContext
getErrorReporter() - Method in interface InputOutputContext: The associated error reporter.
getErrorReporter() - Method in class Outputter
getErrorReporter() - Method in class GraphLogger
getErrorTree() - Method in class ProposerFailureDescription
getExactDepth() - Method in class DirectoryDepth
getException() - Method in exception CheckedStream.ConvertedToRuntimeException
getException(String) - Method in interface NamedProvider: Retrieves the item if it exists, or throws an exception if it doesn't exist.
getException(String) - Method in class LazyEvaluationStore
getException(String) - Method in class SharedFeaturesSubset: Gets a feature by name, throwing an exception if it doesn't exist.
getException(String) - Method in class NamedEntries
getExecutionTime() - Method in class KernelDecision
getExecutionTime() - Method in class Reporting
getExecutionTimeRecorder() - Method in class ExperimentFeedbackContext: Allows execution-time for particular operations to be recorded.
getExecutionTimeRecorder() - Method in class InputOutputContextStateful
getExecutionTimeRecorder() - Method in class ParametersExperiment: Allows execution-time for particular operations to be recorded.
getExecutionTimeRecorder() - Method in class InputManagerParameters: Allows for recording the execution-time of particular operations.
getExecutionTimeRecorder() - Method in interface InputOutputContext: Allows execution-times to be recorded for particular operations.
getExecutionTimeRecorder() - Method in class OutputWriteContext: Records the execution time of particular operations.
getExecutionTimeRecorder() - Method in class ElementOutputter: Records the execution time of particular operations.
getExecutionTimeRecorder() - Method in class FeatureCalculationContext: Records the execution-time of particular operations.
getExperiment() - Method in class ExperimentResultsExperimentStructure
getExperiment() - Method in class ExperimentStructure
getExperimentalManifest() - Method in class ParametersExperiment
getExperimentArguments() - Method in class InputOutputContextStateful
getExperimentArguments() - Method in class ParametersExperiment
getExperimentDescription() - Method in class OptimizationContext
getExperimentIdentifier() - Method in class OutputExperiment: A name for the experiment.
getExperimentIdentifier() - Method in class ParametersExperiment
getExperimentManifest() - Method in class CoupledManifests
getExperimentType() - Method in class FilePathAppendBase: A folder identifying the type of experiment (where the outputs are all put in the same directory
getExperimentType() - Method in class QuickMultiDatasetStructuredExperiment: The value of $1 (see comment above) in naming-structure.
getExperimentType() - Method in class RootedExperiment: A directory identifying the type of experiment.
getExpression() - Method in class RegExSimple: A Java-style regular expression containing groups.
getExpression() - Method in class MatchRegularExpression
getExpression() - Method in class RegularExpression
getExtension() - Method in class FilenameSplitExtension: The extension of the filename.
getExtension() - Method in class OneOrThreeChannelsWriter
getExtension() - Method in class AppendStack
getExtension() - Method in class AppendStackDirect
getExtensions() - Method in class MatchExtensions: A set of file-extensions (without the period), one of which must match the end of a path.
getExtensions() - Method in class BranchExtension: Any extensions to match (case insensitive) not including any leading period.
getExtent() - Method in class KernelPointCursor: The size of the image the kernel iterates over.
getExtractScoreSize() - Method in class DirectAssignMode
getExtractScoreSize() - Method in class UniformProposal
getExtractScoreSizeReport() - Method in class TransformationAssignMode
getExtractScoreSizeState() - Method in class TransformationAssignMode
getExtractWeight() - Method in class KernelInitialMarksFromPartition
getExtraLength() - Method in class Midpoint
getFactor() - Method in class ScoreObjects
getFactor() - Method in class Scale
getFactorHigh() - Method in class Identity
getFactorLow() - Method in class Identity
getFactorStandardDeviation() - Method in class GaussianSampler: Multiples the standard deviation of the distribution found in keyStandardDeviation.
getFallback() - Method in class SpecificPathList: If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown
getFallback() - Method in class ToSuggested: Used as a delegate to calculate the scale if suggestedResize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getFallback() - Method in class RGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallback() - Method in class InferFromHeader: Fallback to use if EXIF information is non-existing or absent.
getFallbackName() - Method in class ExperimentIdentifierAuto: If there's no task-name, then this constant is used as a fallback name
getFeature() - Method in class FeatureProviderDefine: The feature to provide.
getFeature() - Method in class FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session.
getFeature() - Method in class OutputFeatureTable: A list of features to calculate in an evaluation context.
getFeature() - Method in class ScoreObjects: Feature that calculates the score for an object.
getFeature() - Method in class PermuteFeatureBase
getFeature() - Method in class AddCriteriaFeatureRelationThreshold
getFeature() - Method in class FeatureValueCheckMark
getFeature() - Method in class RequireFeatureRelationThreshold
getFeatureCondition() - Method in class IfCondition
getFeatureCondition() - Method in class IfConditionWithinRange: Calculates value for the condition - which is checked if it lies within a certain range
getFeatureElse() - Method in class IfCondition
getFeatureEvaluator() - Method in class MultipleComparer: Calculates the cost used when making assignments.
getFeatureEvaluator() - Method in class ReportFeatureEvaluator
getFeatureEvaluator() - Method in class FeatureCostAssigner
getFeatureEvaluator() - Method in class DiscardOutliers
getFeatureEvaluator() - Method in class RelationWithMatches
getFeatureEvaluator() - Method in class ThresholdedFeature
getFeatureEvaluator() - Method in class ObjectCollectionProviderWithFeature
getFeatureEvaluator() - Method in class MergeGreedyToIncreaseObjectFeature
getFeatureEvaluator() - Method in class MergeToIncreaseObjectFeature
getFeatureEvaluatorMatch() - Method in class RelationWithMatches
getFeatureEvaluatorMerge() - Method in class MergePairs
getFeatureEvaluatorThreshold() - Method in class MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
getFeatureLists() - Method in class FeatureRelatedInitialization: Gets the underlying NamedProviderStore that provides shared-features.
getFeatureNameIndex() - Method in class FeatureInputResults: A mapping from the name of the feature that produced a result, to its index position in results.
getFeatureNames() - Method in class FeatureCalculationContext: The name of each feature being calculated, in identical order, as that is placed in the exported CSV.
getFeatureNames() - Method in class FeatureExporter: The names of the features to be exported.
getFeatureProvider() - Method in class FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
getFeatures() - Method in class FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session
getFeatures() - Method in class ExportFeatures: The features to be exported (after possibly some manipulation or augmentation).
getFeatures() - Method in class SegmentInstanceWithModel: Features to calculate for objects in the features output.
getFeaturesAggregate() - Method in class ExportFeatures: Features applied to each group to aggregate values (accepting FeatureInputResults).
getFeaturesImage() - Method in class PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
getFeatureSource() - Method in class FeatureCalculationContext: The features that are calculated, encapsulated in some object.
getFeaturesPair() - Method in class PairNeighbors: Additional features that are processed on the pair of images (i.e.
getFeatureTables() - Method in class Develop: Specifies a feature-table that can also be outputted.
getFeedbackReceiver() - Method in class FeedbackReceiverRequireArguments
getFeedbackReceiver() - Method in class SegmentWithMarkedPointProcess: Processes feedback from the segmentation algorithm for outputting / debugging.
getFile() - Method in class NamedChannelsInputPart
getFile() - Method in class NamedFile: The file.
getFile() - Method in class SingleFileInputBase
getFile() - Method in class DualPathPredicates: Only accepts files where the predicate returns true
getFileAttributes() - Method in class ImageMetadata: Attributes associated with the file on the filesystem.
getFileExtension() - Method in class FileType
getFileFilter() - Method in class ExperimentResultsExperimentStructure: Files to search for
getFileId() - Method in class AppendCsv: Unique identifier for the stack, object-mask-collection etc.
getFileId() - Method in class FilePathBaseAppendToManagerWithFileID: Unique identifier for the stack, object-mask-collection etc.
getFileInput() - Method in class GroupFiles
getFileInput() - Method in class NamedChannels
getFileInput() - Method in class Stacks
getFileInput() - Method in class QuickExperiment: A string indicating the input file(s)
getFilename() - Method in class PathDifference: The file-name component of the difference, if it exists.
getFileName() - Method in class OutputtedFile
getFileName() - Method in class ReportFeatureForManifestFileBase
getFilePath() - Method in class SortedSetSlice
getFilePath() - Method in class FromSerializedMarks
getFilePath() - Method in class FromSerializedObject
getFilePathParser() - Method in class MultiFileReader
getFilePathProviderSVM() - Method in class FeatureListProviderSVMClassifier
getFilePaths() - Method in class FilePathInitialization: Named-store of file-paths.
getFilePaths() - Method in class FeatureRelatedInitialization: A named-set of file-paths.
getFilePrefix() - Method in class MovieFromSlices
getFiles() - Method in class TraversalResult: All files in any directories that have been traversed.
getFiles() - Method in class ReadFromFile: Provides a single file containing a dictionary.
getFiles() - Method in class FilesProviderUnary
getFiles() - Method in class FilesProviderWithDirectoryUnary
getFiles() - Method in class FromFiles: A provider that should return exactly one File whose path is employed.
getFiles() - Method in class Rooted
getFiles() - Method in class NamedFiles: The files to use as inputs.
getFiles() - Method in class NamedFilesWithDirectory: The files to use as inputs.
getFiles() - Method in class QuickBase: A path to the main channel of each file
getFilter() - Method in class IfObjectFilter
getFilter() - Method in class ObjectCollectionProviderFilterBase
getFilter() - Method in class Filter
getFilter() - Method in class ImageLabellerStringMap
getFilterExtensions() - Method in class InputArguments: If defined, a set of extension filters that can be applied on inputDirectory
getFilterFilesCsv() - Method in class QuickBase: If set, a CSV is read with two columns: the names of images and a
getFilterGlob() - Method in class InputArguments: If defined, a glob that is applied on inputDirectory
getFilterInitialization(Path) - Method in class SharedStateFilteredImageOutput
getFindOutlinePixelAngle() - Method in class TraversePointsOnContour
getFirst() - Method in class CostMatrix: The first set of elements.
getFirst() - Method in class FeatureInputPairObjects
getFirst() - Method in class OutputEnableRulesSpecify: Output-names in the first-level.
getFirst() - Method in class Compose: First transformation from S to U
getFirst() - Method in class PrecalculationOverlay
getFirstArgument() - Method in class HelpConfig: What the application argument is described as in the help message e.g. experimentFile.xml
getFirstBinaryValues() - Method in class ObjectCollection: The BinaryValuesInt associated with the first object in the collection.
getFirstBinaryValuesByte() - Method in class ObjectCollection: The BinaryValuesByte associated with the first object in the collection.
getFloat() - Static method in class VoxelsFactory: A factory that creates voxels of type float.
getFontColor() - Method in class TextStyle: Font-color of drawn text
getFontName() - Method in class TextStyle: Font-name of drawn text
getFontSize() - Method in class TextStyle: Font-size of drawn text
getForAllSlices(int) - Method in class IndexByRegion
getForceReader() - Method in class BioformatsReader: If non-empty forces usage of a particular bioformats plugin.
getFormats() - Method in class InferFromHeader: The formats whose headers will be searched, to find sufficient metadata to populate ImageMetadata.
GetForSeries<T,S> - Interface in org.anchoranalysis.plot
getForSlice(int, int) - Method in class IndexByRegion
getFoundDirectory() - Method in class FinderSingleDirectory
getFoundFile() - Method in class FinderSingleFile
getFriendlyName() - Method in class Feature: A user-friendly human-readable name for the Feature.
getFrom() - Method in class TypedEdge: The vertex the edge joins from.
getFunction() - Method in class ManifestDescription: Identifies the function the entity plays.
getGaussianSigmaMeters() - Method in class AddEdgeFilters
getGenerator() - Method in class BoundOutputter: The generator to be (repeatedly) used to write elements in the sequence.
getGeneratorList() - Method in class CombineRasterGenerator
getGlob() - Method in class MatchGlob: The string describing a glob e.g.
getGlob() - Method in class GlobExtractor.GlobWithDirectory
getGradient() - Method in class ScoreVoxels
getGraphColorScheme() - Method in class PlotIndexBase
getGrayscaleReconstruction() - Method in class MinimaImpositionGrayscaleReconstruction
getGreen() - Method in class RGBColorBean: The green component value of the RGB color.
getGreen() - Method in class RGBColor: The green component value of the RGB color.
getGreen() - Method in class ThreeChannels
getGroup() - Method in class RowLabels: an identifier for a higher-level group which the row belongs to (foreign key)
getGroup() - Method in class AnnotationLabel: Specifies a group for the label (similar labels that are displayed together)
getGroup() - Method in class ExportFeatures: If non-null, this file-path is used to determine the group of the file.
getGroup() - Method in class GroupedStackBase: If defined, translates a file-path into a group.
getGroup() - Method in class CSVRow
getGroup() - Method in class AppendHistogram
getGroupGeneratorName() - Method in class FeatureCalculationContext
getGroupHeaders() - Method in class LabelHeaders: Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
getGroupMap() - Method in class GroupedSharedState
getGroupNum() - Method in class RootFilePathRegEx
getHeaders() - Method in class FeatureCSVMetadata: Headers for the CSV file
getHeaders() - Method in class CSVReader.OpenedCSVFile
getHeight() - Method in class SizeXY: Size in Y dimension.
getHeight() - Method in class ImposeResolution: Physical pixel size of a voxel in y-dimension.
getHistogram() - Method in class HistogramProviderUnary
getHistogram() - Method in class FeatureInputHistogram
getHistogram() - Method in class ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
getHistogram() - Method in class SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
getHistogram() - Method in class PlotHistogram: The histogram to plot.
getHistogram() - Method in class LevelResult
getHistogram() - Method in class FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
getHistogramChannelIndex() - Method in class CalculateLevelBase
getHistogramIndex() - Method in class IdentityImposeValueRelationToHistogram
getHistogramsExtra() - Method in class ScoreVoxels
getHorizontalAlign() - Method in class Overlay
getId() - Method in class DictionaryProviderReference: Unique identifier for the Dictionary to retrieve.
getId() - Method in class Reference: The identifier that uniquely determines the other feature to reference.
getId() - Method in class FeatureProviderReference: The name of the feature to reference.
getId() - Method in class FeatureResultsStatistic: The name of the feature, whose results will provide the statistic.
getId() - Method in class BinarySegmentationReference
getId() - Method in class FilePathProviderReference
getId() - Method in class KernelDecision
getId() - Method in class Reference
getId() - Method in class FromChannel: An shared-objects identifier for a ChannelProvider to use for dimensions.
getId() - Method in class Reference
getId() - Method in class Reference
getId() - Method in class Reference
getId() - Method in class ReferenceOrElse
getId() - Method in class Reference
getId() - Method in class FeatureIntersectingObjects: ID for the particular object-collection
getId() - Method in class ExportFeatures: Translates an input file name to a unique ID.
getId() - Method in class MarkBoundsReference
getId() - Method in class MarkProposerReference
getId() - Method in class MarkMergeProposerReference
getId() - Method in class MarkSplitProposerReference
getId() - Method in class Reference
getId() - Method in class ReferenceOrEmpty
getId() - Method in class CreateEllipse
getId() - Method in class CSVRow
getId() - Method in class Reference
getIdentifier(T, int) - Method in interface IdentifierGetter: Gets the unique identifier.
getIdentifier(T, int) - Method in class IdentifyFromIteration
getIdentifier() - Method in class NamedFile: Unique identifier associated with the file.
getIdentifier(Mark, int) - Method in class IdentifierFromMark
getIdentifier() - Method in class Mark
getIdentifier() - Method in class OverlayMark
getIdentifier() - Method in class KernelWithIdentifier
getIdentifier() - Method in interface Identifiable
getIdentifier(Overlay, int) - Method in class IdentifierFromOverlay
getIdentifier(ObjectWithProperties, int) - Method in class IdentifyDelegateToOverlays
getIdentifier() - Method in class OverlayObjectMask
getIdentifierSubrange() - Method in class InputArguments: If defined, this indicates and specifies only a subset of the naming-elements to use.
getIdentifierSubrange() - Method in class InputContextParameters: If defined, this indicates and specifies only a subset of the naming-elements to use.
getIdentifierSuffix() - Method in class QuickMultiDatasetExperiment
getIdentifierSuffix() - Method in class QuickMultiDatasetStructuredExperiment
getIdGenerator() - Method in class ExportObjectsFromCSV
getIdGetter() - Method in class ObjectDrawAttributes: Gets a unique ID associated with the object
getIfPresent(K) - Method in class LRUCache: Gets an value if present, but doesn't create any new entry if it's absent.
getIgnoreContains() - Method in class AnnotationBackground: If non-empty, to not display any stacks in backgroundStackMap whose name contains this string.
getImage() - Method in class MergedPairsFeatures
getImage() - Method in class PointsInitialization
getImage() - Method in class InitializationWithEnergyStack
getImageDimensions() - Method in class ImageFileShape
getImageLabeller() - Method in class ImageAssignLabel: Maps a label to an image
getImageMetadataReader() - Method in class ConvertNamedChannels: How to read the ImageMetadata from the file-system.
getImgChannelMapCreator() - Method in class GroupFiles
getIncrement() - Method in class SequenceInteger: Size of step to use when incrementing.
getIndex() - Method in interface AssociatedIndex: The associated index.
getIndex() - Method in class Indexable
getIndex() - Method in class ChannelEntry
getIndex() - Method in class KernelPointCursor: The index in the buffer that the kernel currently is focussed on.
getIndex() - Method in class OutputtedFile
getIndex(TreeNode) - Method in class ErrorNodeImpl
getIndex() - Method in class KernelDecision
getIndex() - Method in class AtIndex
getIndex() - Method in class SliceAt: Index in z-dimension of slice to extract
getIndex() - Method in class SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
getIndex() - Method in class IndexedRegionBase
getIndex() - Method in class DistanceIndex
getIndex() - Method in class OrderedRadius
getIndex() - Method in class AsObject
getIndex() - Method in class HOGFeature: Which index to return from the HOG descriptor.
getIndexDay() - Method in class TimestampPattern: The index of the group in regularExpression that encodes the day, starting from 0 for the first group.
getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class FromCSVSharedState
getIndexEnd() - Method in class ExtractSliceRange: Slice index to end extracting from (inclusive).
getIndexForMemo(VoxelizedMarkMemo) - Method in class EnergyMemoList
getIndexHighest() - Method in class DistanceIndexTwice: Highest-level index.
getIndexHours() - Method in class TimestampPattern: The index of the group in regularExpression that encodes the hours, starting from 0 for the first group.
getIndexLowest() - Method in class DistanceIndexTwice: Lowest-level index.
getIndexMinutes() - Method in class TimestampPattern: The index of the group in regularExpression that encodes the minutes, starting from 0 for the first group.
getIndexMonth() - Method in class TimestampPattern: The index of the group in regularExpression that encodes the month, starting from 0 for the first group.
getIndexNonZero() - Method in class SelectSlicesWithIndexBase
getIndexSeconds() - Method in class TimestampPattern: The index of the group in regularExpression that encodes the seconds, starting from 0 for the first group.
getIndexStart() - Method in class ExtractSliceRange: Slice index to start extracting from (inclusive).
getIndexYear() - Method in class TimestampPattern: The index of the group in regularExpression that encodes the year, starting from 0 for the first group.
getIndividual() - Method in class MarksWithEnergyBreakdown
getInitContext() - Method in class FeedbackBeginParameters
getInitialization() - Method in class InitializableBean: The parameters used for initialization.
getInitialization() - Method in class ImageLabellerStringMapInitialization
getInitializationType() - Method in class BeanInitializer: Type of parameters to be propagated, corresponding to P.
getInitialKernel() - Method in class KernelProposer
getInitialPoint() - Method in class ContiguousVoxelPath
getInnerCoreDistance() - Method in class Ellipsoid
getInput() - Method in class AnnotationInputManager: The inputs to be annotated.
getInput() - Method in class InputOutputExperiment: The input-manager to specify where/which/how necessary inputs for the experiment occur.
getInput() - Method in class InputBound
getInput() - Method in class ParametersUnbound
getInput() - Method in class InputManagerUnary: The delegate input-manager which will be circumstantially called by the current input-manager.
getInput() - Method in class ExperimentExecutor
getInput() - Method in class MultiInputManager
getInput() - Method in class AnnotationComparisonInputManager
getInput() - Method in class AnnotationComparisonInput
getInput() - Method in class NamedChannelsAppend
getInput() - Method in class ConvertNamedChannelsToStack
getInput() - Method in class FromCSVInputManager
getInputContext() - Method in class InputManagerParameters
getInputDebug() - Method in class BranchIfDebug: If defined, this provides an input to the manager when in debug-mode, rather than than otherwise inputs.
getInputDirectory() - Method in class FileNamerContext: A directory associated with the inputs, which if defined, is guaranteed to be a parent of them all.
getInputDirectory() - Method in class InputContextParameters: If defined, a directory which can be used by beans to find input
getInputFilterExtensions() - Method in class InputContextParameters: A list of extensions that can be used filter inputs
getInputFilterGlob() - Method in class InputContextParameters: A glob that can be used by beans to filter input
getInputIfPresent(T) - Method in class CacheTransferSource
getInputName() - Method in class MultiInputManager
getInputName() - Method in class SegmentObjectsFromONNXModel: The name of the input in the ONNX model.
getInputName() - Method in class QuickExperiment
getInputName() - Method in class MultiInputManagerQuick
getInputOutput() - Method in class InitializationContext: The input-output context.
getInputOutputContext() - Method in class OptimizationContext
getInputPaths() - Method in class InputContextParameters: A list of paths referring to specific inputs
getInputPointShift() - Method in class ConicFitterBase
getInstance() - Static method in class InterpolatorFactory: Singleton instance of InterpolatorFactory.
getInstanceFor(Class<? extends T>) - Method in class BeanInstanceMap: Gets an instance from the map for a particular family-type.
getInt(int) - Method in class VoxelBuffer: Gets an element from the buffer at a particular position, converting, if necessary, to an int.
getInt(int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Get a value from the buffer at a particular absolute position.
getInt(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Get a value from the buffer at a particular relative position.
getIntensity() - Method in class ScoreVoxels
getIntensityHistogram() - Method in class BinarySegmentationParameters
getIntensityProvider() - Method in class GenerateString
getInterpolator() - Method in class ScaleXY
getInterpolator() - Method in class OutlinePreserveRelativeSize: Interpolator used when scaling the background
getInterpolator() - Method in class ScaleToSize
getItem() - Method in class NamedBean: The item that is to be named, the underlying bean.
getItem() - Method in class DefineSingle: The sole feature that forms the list.
getItem() - Method in class PrependName: Provides the features and names before any prepending.
getItem() - Method in class FeatureUnary
getItem() - Method in class FeatureDeriveFromPair
getItem() - Method in class ReportFeatureWrapError
getItem() - Method in class ThresholdHistogram
getItem() - Method in class DeriveFromPair
getItem() - Method in class FeatureListProviderAggregatePair: For each feature in the list, a corresponding aggregate feature is created in the output list.
getItem() - Method in class Intensity: Feature to apply to the histogram
getItem() - Method in class DerivedObject
getItem() - Method in class FeatureIntersectingObjectsSingleElement
getItem() - Method in class PairedWithMask
getItem() - Method in class RejectIfIntensityLessThan
getItem() - Method in class FeatureSingleObjectFromShared
getItem() - Method in class Intensity: Feature to apply to the histogram
getItem() - Method in class AsObjectMask
getItem() - Method in class QuantileAcrossConnectedComponents
getItem() - Method in class Rooted
getItem() - Method in class CoefficientOfVarianceFromAll
getItem() - Method in class MeanFromAll
getItem() - Method in class Intensity: Feature to apply to the histogram
getItem() - Method in class FeaturePairMemoOne
getItem1() - Method in class FeatureBinary: Provides the first value for the binary-function.
getItem2() - Method in class FeatureBinary: Provides the second value for the binary-function.
getItemMean() - Method in class StatisticalBase
getItemProportionate() - Method in class FeatureAsIndividualProportionate
getItemStdDev() - Method in class StatisticalBase
getIteration() - Method in class Reporting
getIterations() - Method in class AnisotropicDiffusion: How many iterations to perform diffusion.
getIterations() - Method in class MorphologicalOperatorBase
getIterations() - Method in class ObjectCollectionProviderMorphological
getIterations() - Method in class Repeat: The maximum number of iterations.
getIterations() - Method in class Intersection: The number of dilations and erosions to apply to determine if two objects intersect
getIterations() - Method in class IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension.
getIterations() - Method in class Erode
getIterations() - Method in class NumberRemovedVoxelsAfterClosing
getIterations() - Method in class Shell: The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class MorphologicalOperation: iterations for erode, dilate, open, close
getIterations() - Method in class UniformProposal
getIterations() - Method in class NumberIterationsBase: The number of iterations for which the number-of-marks must remain constant.
getIterationsDilation() - Method in class MorphologicalIterations: Number of times to perform morphological dilation
getIterationsErosion() - Method in class MorphologicalIterations: Number of times to perform morphological erosion
getJobDescription() - Method in class SubmittedJob
getJobManifest() - Method in class CoupledManifests
getJobNumber() - Method in class JobDescription
getJobShortName() - Method in class JobDescription
getJobState() - Method in class SubmittedJob
getKappa() - Method in class AnisotropicDiffusion: A parameter kappa associated with the diffusion functions.
getKeep() - Method in class MergeCandidate
getKeepProcessorsFree() - Method in class DebugDependentProcessor: How many processors to avoid using for the tasks.
getKeepProcessorsFree() - Method in class ParallelProcessor: How many processors to avoid using for the tasks.
getKernel() - Method in class KernelWithIdentifier
getKernel() - Method in class WeightedKernel
getKernel() - Method in class OptimizationStep
getKernel() - Method in class Reporting
getKernel() - Method in class KernelProposerOptionSingle
getKernelAccepted() - Method in class Aggregator
getKernelApplication() - Method in class DilationContext: How the kernel is applied to the scene.
getKernelCalcContext() - Method in class TransformationContext
getKernelFactoryList() - Method in class FeedbackBeginParameters
getKernelHalfWidth() - Method in class Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
getKernelNegative() - Method in class KernelProposerOptionDual
getKernelNoProposalDescription() - Method in class Reporting
getKernelPositive() - Method in class KernelProposerOptionDual
getKernelProposed() - Method in class Aggregator
getKernelProposer() - Method in class SegmentWithMarkedPointProcess: Proposes kernel-changes during iterations of hte marked-point-processes.
getKernelStateBridge() - Method in class TransformationAssignMode
getKey() - Method in exception GetOperationFailedException: The key that was used in the operation that created this exception.
getKey() - Method in class AssignFromDictionary: The key of the value in the dictionary that will be assigned.
getKey() - Method in class DictionaryCondition: The key in the dictionary whose value is checked.
getKey() - Method in class IfParamEqual
getKey() - Method in class ParamFromCollection: The name of the key in the dictionary, whose corresponding value will be returned.
getKey() - Method in class FilePathParser
getKey() - Method in class RegularExpression
getKey() - Method in class FromDictionary
getKeyGroupID() - Method in class RegularExpression
getKeyLower() - Method in class ScaleByDictionary
getKeyMean() - Method in class GaussianSampler: The name of the key in the dictionary with the mean of the distribution.
getKeyPrefix() - Method in class FromDictionary: Prefix prepended to key
getKeyStandardDeviation() - Method in class GaussianSampler: The name of the key in the dictionary with the standard-deviation.
getKeySuffix() - Method in class FromDictionary
getKeyUpper() - Method in class ScaleByDictionary
getLabel() - Method in class ImageLabelAnnotation: The label that applies to the image.
getLabel() - Method in class StackProviderWithLabel
getLabelMap() - Method in class ImageCSVLabellerInitialization
getLabels() - Method in class LabelledResultsVector: The labels.
getLabels() - Method in class PlotIndexBase
getLabels() - Method in class ImageLabelStrategy
getLabels() - Method in class LabelledResultsVectorWithThumbnail: The labels.
getLastDivider() - Method in class Aggregator
getLastPoints1() - Method in class MarkMergeProposer
getLastPoints2() - Method in class MarkMergeProposer
getLeafDirectories() - Method in class TraversalResult: All the directories in the bottom-most depth that was traversed.
getLeft() - Method in class ObjectsToCompare: Objects on left-side of the comparison
getLeftUnassigned() - Method in class OverlappingObjects: The unassigned objects in the left set.
getLevel() - Method in class Constant
getLevel() - Method in class LevelResult
getLine() - Method in class CSVRow
getList() - Method in class Concatenate
getList() - Method in class RegExList: The list of RegExes that are successively tried to be matched.
getList() - Method in class StringMap: A list of mappings between a single-items in the respective sets.
getList() - Method in class ToMultiple: The list of loggers to log to
getList() - Method in class MessageLoggerList
getList() - Method in class Define: The list that specifies features.
getList() - Method in class DefinedNamed: A list of FeatureListProviders with an associated name.
getList() - Method in class FeatureList: The list of features.
getList() - Method in class FeatureFromList: The features whose results will be somehow combined, to form the result of this class.
getList() - Method in class ArrangeRaster
getList() - Method in class Combine
getList() - Method in class TileWithLabels
getList() - Method in class FinderExperimentFileDirectories
getList() - Method in class RegionMap
getList() - Method in class AddCriteriaOr
getList() - Method in class FeedbackReceiverList
getList() - Method in class TerminationConditionListOr
getList() - Method in class Concatenate: A list of ColorProvider to be concatenated.
getList() - Method in class CalculateLevelListBase
getList() - Method in class ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
getList() - Method in class Concatenate
getList() - Method in class Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
getList() - Method in class Concatenate
getList() - Method in class SpecificAndRename
getList() - Method in class FromEntries
getList() - Method in class Combine
getList() - Method in class Concatenate: The list of InputManagers that will be concatenated.
getList() - Method in class SummarizerAggregate
getList() - Method in class AndList
getList() - Method in class VisitSchedulerAnd
getList() - Method in class VisitSchedulerUniformSample
getList() - Method in class MarkProposerFromList
getListAdditionalChannelProviders() - Method in class ScoreObjects
getListAppend() - Method in class NamedChannelsAppend
getListAppend() - Method in class MultiInputManagerQuick: Additional entities that are appended to the multi-input
getListFeatures() - Method in class BinaryClassifierImageLabeller
getListFromManager(MultiInputManager) - Method in class AppendDictionary
getListFromManager(MultiInputManager) - Method in class AppendFilePath
getListFromManager(MultiInputManager) - Method in class AppendHistogram
getListFromManager(MultiInputManager) - Method in class AppendMarks
getListFromManager(MultiInputManager) - Method in class AppendObjects
getListFromManager(MultiInputManager) - Method in class AppendStack
getListFromManager(MultiInputManager) - Method in class AppendStackDirect
getListFromManager(MultiInputManager) - Method in class FilePathBaseAppendToManager
getListImageFeatures() - Method in class EnergySchemeCreatorByElement
getListImageFeatures() - Method in class EnergyScheme
getListPaths() - Method in class SpecificPathList: If specified, this forms the list of paths which is provided as input.
getListReportFeatures() - Method in class ExportReportFeatures
getListStackProvider() - Method in class ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
getListStackProviderMIP() - Method in class ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
getLocal(int) - Method in interface BufferRetriever: Get a buffer at a particular index in the z-dimension.
getLocal(int) - Method in class LocalSlices
getLocalPath() - Method in class AnchorBean: A local path on the filesystem associated with this bean (from serialization) if defined.
getLog() - Method in class OnlyIf: The logger to use if conditions are fulfilled
getLogExperiment() - Method in class OutputExperiment: Where log messages that do not pertain to a specific job (input) appear.
getLogExperimentPath() - Method in class QuickMultiDatasetExperiment: Relative path to a logger for the experiment in gneeral
getLogger() - Method in class InitializableBean: The logger.
getLogger() - Method in class CommonContext: The logger
getLogger() - Method in class InitializationContext
getLogger() - Method in class InputBound
getLogger() - Method in class InputOutputContextStateful
getLogger() - Method in class InputManagerParameters
getLogger() - Method in class FileNamerContext: Logs information messages.
getLogger() - Method in interface InputOutputContext: The associated logger.
getLogger() - Method in class ReporterAggregate
getLogger() - Method in class FeedbackEndParameters
getLogger() - Method in class OptimizationContext
getLogger() - Method in class TransformationContext
getLogger() - Method in class FeatureCalculationContext
getLoggerExperiment() - Method in class ExperimentFeedbackContext: The logger associated with the experiment.
getLoggerExperiment() - Method in class ParametersExperiment
getLoggerTaskCreator() - Method in class ParametersExperiment: This is a means to create new log-reporters for each task.
getLogReporterJob() - Method in class InputBound
getLogTask() - Method in class InputOutputExperiment: Where log messages that do pertain to a specific job (input) appear.
getLogTaskPath() - Method in class QuickMultiDatasetExperiment: Relative path to a logger for a specific task
getMainChannelIndex() - Method in class NamedChannelsQuick: Index of the mainChannel
getMainChannelName() - Method in class NamedChannelsQuick: The name of the channel provided by the rasters in file Provider
getMainObjectName() - Method in class MultiInput
getMainObjectName() - Method in class StackWithMap
getMajorAxisAngle() - Method in class EllipseStandardFormConverter
getMajorAxisSlope() - Method in class EllipseStandardFormConverter
getManifest() - Method in class InputBound
getManifestDescription() - Method in class OutputPattern: A manifest-description for the directory, if defined.
getManifestDescription() - Method in class FileType
getManifestDescriptionFunction() - Method in class MarksGeneratorBase
getManifestDeserializer() - Method in class CoupledManifestsInputManager
getManifestExperimentInputFileSet() - Method in class CoupledManifestsInputManager
getManifestFunction() - Method in class ObjectSerializerPeriodicReporter
getManifestFunction() - Method in class VoxelizedMarksChangeReporter
getManifestInputFileSet() - Method in class CoupledManifestsInputManager
getMap() - Method in class OperationMap
getMap() - Method in class OverlayProperties
getMap() - Method in class ImageLabellerStringMap
getMap() - Method in class ImageLabellerStringMapInitialization
getMapping() - Method in class AnonymizeSharedState
getMark() - Method in class FeatureInputMark
getMark() - Method in class VoxelizedMarkMemo: The associated mark
getMark() - Method in class OverlayMark
getMark() - Method in class KernelDeath.MarkAnd
getMark() - Method in class ObjectWithEllipse
getMarkBounds() - Method in class MarkBoundsDefine
getMarkBounds() - Method in class SegmentThresholdAboveMinBound
getMarkEvaluator() - Method in class MarkProposerStrategy: A mark-evaluator that is added to the GUI to support this annotation
getMarkFactory() - Method in class MarkEvaluator
getMarkFactory() - Method in class KernelCalculationContext
getMarkFactory() - Method in class MarkFactoryContext
getMarkFactory() - Method in class OptimizationContext
getMarkFactory() - Method in class SegmentWithMarkedPointProcess: Creates a new mark, before perhaps further manipulations by a kernel.
getMarkFactory() - Method in class FitPointsFromObjects
getMarkFromMarksProposer() - Method in class KernelSplit
getMarkProposer() - Method in class MarkProposerStrategy: Name of the MarkProposer to use.
getMarkProposer() - Method in class FromMarkProposer
getMarkProposer() - Method in class MergeMarkEllipse
getMarkProposer() - Method in class KernelBirthAndKill
getMarkProposer() - Method in class KernelExchange
getMarkProposer() - Method in class KernelBirthVoxelized
getMarkProposerAdditionalBirth() - Method in class KernelBirthAndKill
getMarkProvider() - Method in class CreateMarkFromPoints
getMarkProvider() - Method in class ReportFeatureOnMark
getMarkProvider() - Method in class FromSingleMark
getMarkProvider() - Method in class RequireFeatureRelationThreshold
getMarkRmv() - Method in class KernelDeath
getMarks() - Method in class RandomCollectionWithAddCriteria
getMarks() - Method in class FeatureInputMarkCollection
getMarks() - Method in class IndexableMarksWithEnergy
getMarks() - Method in class MarksWithEnergyBreakdown
getMarks() - Method in class MarksWithTotalEnergy: The marks
getMarks() - Method in class VoxelizedMarksWithEnergy
getMarks() - Method in class ReportFeatureOnMarks
getMarks() - Method in class MarksWithDisplayStack
getMarks() - Method in class ColoredMarks
getMarks() - Method in class MarkCollection: The underlying List that stores the Marks in the collection.
getMarks() - Method in class FromMarks
getMarks() - Method in class ScaleXY
getMarks() - Method in class RetrieveSingleMarkOnly
getMarks() - Method in class ColoredMarks
getMarks() - Method in class MarksFromPartition
getMarksAfter() - Method in class Reporting
getMarksAfterOptional() - Method in class Reporting
getMarksColored() - Method in class ColoredMarksWithDisplayStack
getMarksProposer() - Method in class KernelInitialMarksFromPartition
getMarksProposer() - Method in class KernelInitialMarksProposed
getMarksProposer() - Method in class KernelInitialMarksVoxelized
getMarksReject() - Method in class DualMarksAnnotation: Marks covering area that should be rejected, can be null
getMarksWithTotalEnergy() - Method in class MarksWithEnergyBreakdown
getMask() - Method in class MaskProviderUnary
getMask() - Method in class FromMaskBase
getMask() - Method in class UnaryWithMaskBase
getMask() - Method in class ScoreVoxels
getMask() - Method in class FromChannel
getMask() - Method in class SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
getMask() - Method in class ConnectedComponentsFromMask
getMask() - Method in class AndObjectsWithMasks
getMask() - Method in class FromMask
getMask() - Method in class SegmentChannel
getMask() - Method in class ColoredMask
getMask() - Method in class FromChannelOrMask: A mask that is provided to the stack.
getMask() - Method in class PairedWithMask
getMask() - Method in class MaskAsSingleObject
getMask() - Method in class FillHoles
getMask() - Method in class CheckMarkWithMask
getMask() - Method in class FindPointOnContourWalk
getMask() - Method in class XYOrientationExtendToZ
getMaskContour() - Method in class TraverseOuterContourOnImage
getMaskElse() - Method in class IfPredicateBase: Returned instead of mask if the predicate is not satisfied
getMaskFilled() - Method in class TraverseOuterContourOnImage
getMaskFilled() - Method in class XYOrientationExtendToZ
getMaskIndex() - Method in class SurfaceSizeMaskNonZero
getMaskValue() - Method in class ExportImageHistograms: What voxel value to read as "On" in the mask above.
getMaskValue() - Method in class OverlapMaskBase
getMatch() - Method in class FilterCSVColumn
getMatch() - Method in class MatchedAppendCsv
getMatcher() - Method in class SearchDirectory
getMatcher() - Method in class MatchExtensions
getMatcher() - Method in class RelationWithMatches
getMatcher() - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
getMatcher() - Method in class Match
getMatches() - Method in class MatchedObject: The matches associated with the source-object
getMatrix() - Method in class CostMatrix: A two-dimensional array mapping the costs from first to second.
getMatrix() - Method in class RotationMatrix: The underlying matrix used internally in the rotation-matrix.
getMax() - Method in interface Progress: Retrieves the maximum value of progress that is possible.
getMax() - Method in class ProgressConsole
getMax() - Method in class ProgressIgnore
getMax() - Method in class ProgressIncrement: Retrieves the maximum value of progress that is possible.
getMax() - Method in class BoundMinMax
getMax() - Method in class ResolvedBound
getMax() - Method in class PointListBase
getMax() - Method in class ScaleByMinMaxValue
getMax() - Method in class ClampHistogramMax
getMax() - Method in class UnitsWithinRange: Maximum-boundary for acceptable range
getMax() - Method in class OutsideRange
getMax() - Method in class MaxOverlapRatio
getMax() - Method in class InvertedMax
getMax() - Method in class CompareWithRangeFeature: Calculates maximally-allowed range boundary
getMax() - Method in class RangeCompareFromScalars: Boundary value indicating maximally-allowed range value
getMaxCost() - Method in class MultipleComparer: The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
getMaxCost() - Method in class FeatureCostAssigner
getMaxDirectoryDepth() - Method in class SearchDirectory: If non-negative the max depth of directories.
getMaxDirectoryDepth() - Method in class PathMatchConstraints: Limits on the depth of how many sub-directories are recursed
getMaxDirectoryDepth() - Method in class ExperimentResultsExperimentStructure
getMaxDistance() - Method in class MergeWithOptionalDistanceConstraint: An optional maximum distance
getMaxDistance() - Method in class CostOverlapWithinMidpointDistance
getMaxDistance() - Method in class FindPointOnContourWalk
getMaxDistanceBetweenMinima() - Method in class AddDistanceTransform
getMaxDistanceCOG() - Method in class MergeSpatialClusters: The maximum distance allowed between center-of-gravities of objects
getMaxDistanceDeltaContour() - Method in class AddDistanceTransform: The maximum distance allowed between two seeds in terms of their values in the distance map
getMaxDistanceDeltaContour() - Method in class MergeSpatialClusters: The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
getMaxDistanceProposer() - Method in class VisitSchedulerMaxDistanceAlongContour
getMaxDistanceZ() - Method in class XYOrientationExtendToZ
getMaximumIndex() - Method in interface IndexRange: The maximum index in the range.
getMaximumNumberChannels() - Method in class IntensityMoments: An upper limit on the number of channels in the energy-stack for which we create features.
getMaxInstant() - Method in class ClusterIdentifier: Maximum timestamp in cluster.
getMaxIter() - Method in class Repeat
getMaxIter() - Method in class Repeat
getMaxIter() - Method in class Repeat
getMaxIter() - Method in class RadiiProposerRepeat
getMaxNumberItems() - Method in class Limit
getMaxNumberItems() - Method in class Limit
getMaxNumberProcessors() - Method in class TaskArguments: Suggests a maximum number of processors (CPUs) for a task.
getMaxNumberProcessors() - Method in class DebugDependentProcessor: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class ParallelProcessor: Theoretical maximum number of (CPU) processors to use in parallel.
getMaxNumberProcessors() - Method in class QuickMultiDatasetExperiment: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class QuickMultiDatasetStructuredExperiment
getMaxNumItems() - Method in class LimitWithDirectory
getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
getMaxResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
getMaxSize() - Method in class Mser
getMaxSplitGroups() - Method in class CompareAnnotations
getMaxTime() - Method in class ClusterIdentifier: Gets the latest date-time in the cluster.
getMaxValue() - Method in class Histogram: Maximum possible value in the histogram (inclusive).
getMaxValue() - Method in class ConsistentChannelChecker
getMaxVar() - Method in class Mser
getMaxVolume() - Method in class FillHoles
getMaxX() - Method in class Box: Maximum X coordinate inclusive.
getMaxY() - Method in class Box: Maximum Y coordinate inclusive.
getMaxZ() - Method in class Box: Maximum Z coordinate inclusive.
getMean() - Method in class MeanScale: The mean.
getMean(int) - Method in class ImageMoments: Get the mean-value for a particular axis.
getMedianRadiusMeters() - Method in class AddEdgeFilters
getMemoForIndex(int) - Method in class VoxelizedMarksWithEnergy
getMemoForIndex(int) - Method in class EnergyMemoList
getMemoForIndex(int) - Method in class MemoList
getMemoForIndex(int) - Method in interface MemoForIndex
getMemoForMark(Mark) - Method in class VoxelizedMarksWithEnergy
getMemoForMark(MarkCollection, Mark) - Method in class EnergyMemoList
getMemoized() - Method in class FinderSerializedObject: Provides a memoized (cached) means of access the results of the finder
getMerge() - Method in class MergeCandidate
getMerged() - Method in class FeatureInputPairObjects: Returns a merged version of the two-objects available (or null if not available)
getMergedOptional() - Method in class FeatureInputPairObjects
getMergedPosTolerance() - Method in class MergeMarkEllipse
getMergeMarkProposer() - Method in class KernelMerge
getMessage() - Method in exception GetOperationFailedException: A message describing the failure.
getMessage() - Method in class ReportFeatureWrapError
getMessageLogger() - Method in class InputOutputContextStateful: Exposed as StatefulMessageLogger rather than as MessageLogger that is found in Logger
getMessageNoInputs() - Method in class InputOutputExperiment: A message written to the logger if no inputs exist for the experiment, and it thus ends early.
getMessageReporter() - Method in interface InputOutputContext: The associated message reporter.
getMessages() - Method in class ConvertedInput: Any messages written to the log during conversion.
getMetadata() - Method in class FeatureInputImageMetadata: The image metadata.
getMethod() - Method in class AutoLocalThreshold
getMethod() - Method in class ThresholderAutoIJ: One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
getMethod() - Method in class CopyFiles: How the copying occurs from source to destination file.
getMin() - Method in interface Progress: Retrieves the minimum value of progress that is possible.
getMin() - Method in class ProgressConsole
getMin() - Method in class ProgressIgnore
getMin() - Method in class ProgressIncrement: Retrieves the minimum value of progress that is possible.
getMin() - Method in class BoundMinMax
getMin() - Method in class ResolvedBound
getMin() - Method in class PointListBase
getMin() - Method in class ScaleByMinMaxValue
getMin() - Method in class UnitsWithinRange: Minimum-boundary for acceptable range
getMin() - Method in class OutsideRange
getMin(Function<FileDetails, Optional<Integer>>) - Method in class ParsedFilePathBag
getMin() - Method in class RadiiMinRatio
getMin() - Method in class CompareWithRangeFeature: Calculates minimally-allowed range boundary
getMin() - Method in class RangeCompareFromScalars: Boundary value indicating minimally-allowed range value
getMinConfidence() - Method in class ThresholdConfidence: The minimum confidence of an element for its object-mask to be initially included for consideration (before merging).
getMinConfidence() - Method in class DecodeMaskRCNN: Only proposals outputted from the model with a score greater or equal to this threshold are considered.
getMinConfidence() - Method in class DecodeEAST: Proposed bounding boxes below this confidence interval are removed from consideration.
getMinDiff() - Method in class MeanIntensityDifference
getMinDifference() - Method in class Difference: A minimum difference, below which 0.0 is returned
getMinDifference() - Method in class DifferenceCalculateLevelStandardDeviation
getMinDiversity() - Method in class Mser
getMinimaImposition() - Method in class ImposeMinima
getMinimumBoundingBoxVolume() - Method in class FloodFillEachIntensityLevel: Only objects whose bounding-box volume is greater or equal to this threshold are included.
getMinimumIndex() - Method in interface IndexRange: The minimum index in the range.
getMinimumPerCluster() - Method in class ClusterByTimestamp: The minimum number of files that must exist for a cluster.
getMinInstant() - Method in class ClusterIdentifier: Minimum timestamp in cluster.
getMinIntensity() - Method in class RejectIfIntensityLessThan
getMinIntensity() - Method in class ThresholderSimpleFillHoles2D: Intensity for thresholding
getMinIntensityValue() - Method in class MorphologicalOperatorBase
getMinMaskValue() - Method in class DecodeMaskRCNN: Only voxels with a value greater or equal to this threshold are considered as part of the mask.
getMinMaxIgnoreBeforeIndex() - Method in class LinePlot
getMinNumberObjects() - Method in class DiscardOutliers
getMinNumberPoints() - Method in class SplitContourAtSaddlePoints: If a contour has less than this number of points, we don't split it, and return it as-is
getMinNumberVoxels() - Method in class SplitIntoSquares: Only includes squares that have at least this number of voxels.
getMinNumberVoxels() - Method in class ConnectedComponentsFromBinarySegmentation
getMinNumberVoxels() - Method in class ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
getMinNumPoints() - Method in class CreateMarkFromPoints
getMinNumPoints() - Method in class PointsFitterToMark: If an object has fewer points than before being fitted, we ignore
getMinNumSlices() - Method in class XYOrientationExtendToZ
getMinNumZSlices() - Method in class AtLeastZSlices
getMinorAxisAngle() - Method in class EllipseStandardFormConverter
getMinorAxisSlope() - Method in class EllipseStandardFormConverter
getMinOverlap() - Method in class CostOverlapWithinMidpointDistance
getMinRadius() - Method in class LinearLeastSquaresEllipseFitter
getMinRadius() - Method in class LinearLeastSquaresEllipsoidFitter
getMinRatio() - Method in class DiscardOutliers
getMinResolution() - Method in class MinimumXYResolution
getMinResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
getMinResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
getMinResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
getMinResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
getMinSize() - Method in class Mser
getMinTime() - Method in class ClusterIdentifier: Gets the earliest date-time in the cluster.
getMinusOne() - Method in class SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index -1 or null if it's the first slice.
getMinVal() - Method in class FeatureValueCheckMark
getMinVolume() - Method in class ConnectedComponentsFromMask
getMinVolume() - Method in class VolumeMin
getMinVolumeConnectedComponent() - Method in class AddDistanceTransform
getMinX() - Method in class Box: Minimum X coordinate inclusive.
getMinY() - Method in class Box: Minimum Y coordinate inclusive.
getMinZ() - Method in class Box: Minimum Z coordinate inclusive.
getModelBinaryPath() - Method in class SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.
getModelDirectory() - Method in class CommonContext: Directory where machine-learning models can be found
getModelDirectory() - Method in class InputArguments
getModelDirectory() - Method in class InputOutputContextStateful
getModelDirectory() - Method in class ImageInitialization
getModelDirectory() - Method in interface InputOutputContext: An input-directory in which models are stored.
getModelDirectory() - Method in class FeatureCalculationContext
getModelPath() - Method in class SegmentObjectsFromONNXModel: Relative-path to the model file in ONNX form, relative to the models/ directory in the Anchor distribution.
getModelPool() - Method in class SharedStateSegmentInstance
getModelTextGraphPath() - Method in class SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.
getModificationTime() - Method in class ImageFileAttributes: The last modified timestamp on the file the image was loaded from.
getMultipleComparer() - Method in class MarkProposerStrategy
getMultipleOf() - Method in class FitTo: The eventual width and height of the image must be a multiple of this number.
getMultiplyBy() - Method in class DistanceTransform3D
getName() - Method in class FromXMLList: The name of the file in the current working directory WITHOUT THE .xml EXTENSION
getName() - Method in class NamedBean: The name associated with item.
getName() - Method in class RootPath: The name of the root-path, which need not be unique in itself.
getName() - Method in interface NameValue: The associated name.
getName() - Method in class SimpleNameValue
getName() - Method in class ExperimentIdentifierConstant
getName() - Method in class ChannelEntry
getName() - Method in class OptionalNameValue: An optional-name.
getName() - Method in class IncreasingIntegers
getName() - Method in class IncrementingIntegers
getName() - Method in class SequenceType
getName() - Method in class StringsWithoutOrder
getName() - Method in class NamedPath: A unique name associated with the path
getName() - Method in class Circle
getName() - Method in class Ellipse
getName() - Method in class Ellipsoid
getName() - Method in class Sphere
getName() - Method in class Mark
getName() - Method in class LineSegment
getName() - Method in class PointList
getName() - Method in class Polygon
getName() - Method in class PolygonCurve
getName() - Method in class RotatableBoundingBox
getName() - Method in class Kernel
getName() - Method in class WeightedKernel
getName() - Method in class NamedChannel
getName() - Method in class AdjacentFile: A name to describe the adjacent file
getName() - Method in class FilePathAppendBase: The name of the appended entity
getNameLeft() - Method in class AnnotationComparisonInputManager
getNamer() - Method in class GroupFiles
getNamer() - Method in class RemoveExtension
getNamer() - Method in class SubsetRangeIfRequested: The namer that is called to provide names that are subsetted.
getNamer() - Method in class NamedFilesBase
getNamer() - Method in class QuickBase: Assigns each input a unique compact name.
getNameRight() - Method in class AnnotationComparisonInputManager
getNames() - Method in class StatisticsToExport: The names of statistics describing the annotation-comparison, as produced by StatisticsToExport.getValues().
getNames() - Method in class NamedFeatureCalculatorMulti
getNames() - Method in class AnnotationComparisonInput
getNameSubrange() - Method in class FileNamerContext: If defined, this indicates and specifies only a subset of the naming-elements to use.
getNaming() - Method in class CopyFiles: How an output name (and path) is selected for an input file.
getNamingSharedState() - Method in class RecordingCounter
getNavigateHigherDirectories() - Method in class MultiFileReader: Search x number directories higher than file.
getNoProposalReason() - Method in class KernelDecision
getNumberBins() - Method in class HOGParameters: The number of bins in each histogram for a cell.
getNumberChannels() - Method in class EnergyStack: The number of channels in the stack.
getNumberChannels() - Method in class EnergyStackWithoutParameters: The number of channels in the stack.
getNumberChannels() - Method in class DisplayStack: The number of channels in the stack.
getNumberChannels() - Method in class ImageMetadata: The number of channels in the image.
getNumberChannels() - Method in class Stack: The number of channels in the stack.
getNumberChannels() - Method in class StackNotUniformSized: The number of channels in the Stack.
getNumberChannels() - Method in class ScaleableBackground: Number of channels in the stack
getNumberChannels() - Method in class ForceNumberChannels
getNumberChannels() - Method in class ImageFileShape
getNumberChannelsPerArray() - Method in class ImageFileEncoding: The total number of channels found in any one buffer.
getNumberColors() - Method in class TiffTimeSeries
getNumberColumns() - Method in class Tile: The number of columns to use in the table produced when tiling.
getNumberConverter() - Method in class AnonymizeSharedState
getNumberDecimalPlaces() - Method in class FeatureCostAssigner
getNumberDigits() - Method in class IncrementingNumber: Number of digits in the number, with leading zeros as necessary.
getNumberDilations() - Method in class LevelPerObjectIndependently
getNumberDimensions() - Method in class RotationMatrix: The number of dimensions in the rotation-matrix.
getNumberElements() - Method in class IncreasingIntegers
getNumberElements() - Method in class IncrementingIntegers
getNumberElements() - Method in class SequenceType
getNumberElements() - Method in class StringsWithoutOrder
getNumberFrames() - Method in class ImageMetadata: The number of frames (separate images representing different points in a time-series) in the image.
getNumberFrames() - Method in class ForceNumberFrames
getNumberFrames() - Method in class ImageFileShape
getNumberGPUProcessors() - Method in class ParallelProcessor: How many GPU processors to use when this is possible as a substitute for a CPU processor
getNumberKernels() - Method in class KernelProposer
getNumberLevelsGrouping() - Method in class CompareAnnotations
getNumberLoopPoints() - Method in class SplitContourAtSaddlePoints
getNumberParentOperations() - Method in class RecordedExecutionTimes.RecordedOperation: The number of parent operations.
getNumberParentOperations() - Method in class RunningSumParented: The number of parent operations.
getNumberPoints() - Method in class LinePlot
getNumberRows() - Method in class Tile: The number of rows to use in the table produced when tiling.
getNumberSeries() - Method in class PlotIndexBase
getNumberSlices() - Method in class ImageFileShape
getNumberSubdirectories() - Method in class LastDirectories: How many directories to include in the name.
getNumCols() - Method in class TileWithLabels
getNumColsUsed() - Method in class TableItemArrangement
getNumMarks() - Method in class FromMarkProposer
getNumRowsUsed() - Method in class TableItemArrangement
getObject() - Method in class Found: The found object.
getObject() - Method in class FeatureInputSingleObject
getObject() - Method in class OverlayObjectMask
getObject() - Method in class LevelResult
getObject() - Method in class ObjectVertex
getObject() - Method in class ObjectWithEllipse
getObject1() - Method in class FeatureInputPairMemo
getObject2() - Method in class FeatureInputPairMemo
getObjectMatcher() - Method in class Bridge: Used to match each intermediary-object to a final-object
getObjects() - Method in class ObjectCollectionProviderUnary
getObjects() - Method in class FeatureInputObjectCollection
getObjects() - Method in class OutputFeatureTable: The objects for which features are calculated.
getObjects() - Method in class ReportFeatureOnObjectsBase
getObjects() - Method in class DistanceTransformForEachObject3D
getObjects() - Method in class LevelPerObjectBase: The objects for whom a level is calculated
getObjects() - Method in class UnaryWithObjectsBase
getObjects() - Method in class GenerateToMatchObjects
getObjects() - Method in class FromObjects
getObjects() - Method in class IntersectsWith
getObjects() - Method in class Always
getObjects() - Method in class Intersection
getObjects() - Method in class Permute
getObjects() - Method in class ColoredObjects: Objects to draw on a background
getObjects() - Method in class ObjectAggregationBase
getObjects() - Method in class ColoredObjectCollection: The objects in the collection.
getObjects() - Method in class FromObjects
getObjects() - Method in class ObjectAsPoints
getObjects() - Method in class IncludeRandomObjects
getObjects() - Method in class PointsFromObjects
getObjects() - Method in class FromObjects
getObjects() - Method in class ExportObjectsBase
getObjects() - Method in class PointsFitterToMark
getObjects1() - Method in class MergeTwoCollectionsItemwise: First collection with items to be merged
getObjects2() - Method in class MergeTwoCollectionsItemwise: Second collection with items to be merged
getObjectsBlue() - Method in class ThreeColoredObjects
getObjectsContainer() - Method in class WithContainerBase
getObjectsElse() - Method in class ReferenceOrElse
getObjectsGreater() - Method in class GreaterIntersectionWith
getObjectsGreen() - Method in class ThreeColoredObjects
getObjectsGrouped() - Method in class FilterByGroup
getObjectsLesser() - Method in class GreaterIntersectionWith
getObjectsRed() - Method in class ThreeColoredObjects
getObjectsRejected() - Method in class ObjectCollectionProviderFilterBase
getObjectsSeeds() - Method in class SegmentChannel
getObjectsSeeds() - Method in class SegmentWithSeeds
getObjectsSource() - Method in class AssignFromIntersectingObjects
getObjectsSource() - Method in class SegmentWithSeeds
getObjectsSplitBy() - Method in class SplitByObjects
getObjectsTarget() - Method in class AssignFromIntersectingObjects
getOff() - Method in class BinaryValuesByte: The byte representation of the value for off.
getOff() - Method in class BinaryValuesInt: The integer representation of the value for off.
getOffset() - Method in class ClusterIdentifier: The offset to assume the time-stamp belongs in.
getOn() - Method in class BinaryValuesByte: The byte representation of the value for on.
getOn() - Method in class BinaryValuesInt: The integer representation of the value for on.
GetOperationFailedException - Exception in org.anchoranalysis.core.index: When a get operation fails for a particular key.
GetOperationFailedException(Exception) - Constructor for exception GetOperationFailedException: Creates with only a cause, omitting a key and a message.
GetOperationFailedException(int, String) - Constructor for exception GetOperationFailedException: Creates with a message, but no cause - with an integer key.
GetOperationFailedException(String, String) - Constructor for exception GetOperationFailedException: Creates with a message, but no cause - with a String key.
GetOperationFailedException(int, Throwable) - Constructor for exception GetOperationFailedException: Creates with a cause, but no message - with an integer key.
GetOperationFailedException(String, Throwable) - Constructor for exception GetOperationFailedException: Creates with a cause, but no message - with a String key.
getOperationIdentifier() - Method in class RecordedExecutionTimes.RecordedOperation: An (unique) identifier for the operation.
getOptimization() - Method in class SegmentWithMarkedPointProcess: The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
getOptional(String) - Method in interface NamedProvider: Retrieves the item if it exists, or returns Optional.empty() if it doesn't exist.
getOptional(String) - Method in class NamedProviderBridge
getOptional(String) - Method in class NamedProviderCombine
getOptional(String) - Method in class NameValueMap
getOptional(String) - Method in class EagerEvaluationStore
getOptional(String) - Method in class LazyEvaluationStore
getOptional(String) - Method in class SharedFeatures
getOptional(String) - Method in class NamedStacks
getOptional(String) - Method in class WrapStackAsTimeSequenceStore
getOptionList() - Method in class KernelProposer
getOptions() - Method in class BioformatsReader: Options that influence how stack is read.
getOptions() - Method in class ReadOptionsDelegate
getOrCalculate(T) - Method in class ResolvedPart: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class ResolvedPartMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from a previous execution.
getOrCalculate(T) - Method in class CalculationPart: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class CalculationPartMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from a previous execution.
getOrCreate(Class<?>) - Method in class SharedObjects: Gets an existing store, or creates a new one
getOrientation() - Method in class Ellipse
getOrientation() - Method in class Ellipsoid
getOrientationProposer() - Method in class OrientationAndRadiiProposer
getOrientationXYProposer() - Method in class XYOrientationExtendToZ
getOriginal() - Method in class OverlappingObject: Original unscaled element before any operations
getOrLog(String, Logger) - Method in interface Findable: Gets an object or otherwise logs a message describing what went wrong.
getOrLog(String, Logger) - Method in class Found
getOrLog(String, Logger) - Method in class NotFound
getOrNull(U) - Method in class CalculationPartMap: Gets an existing result for the current input from the cache.
getOtherwise() - Method in class IfRelativeToDirectory: The namer to use if the relative-to-directory option is not selected.
getOutlineColor() - Method in class SegmentInstanceWithModel: The color of the outline.
getOutlinePixelsRetriever() - Method in class TraversePointsOnContour
getOutlinePixelsRetrieverReverse() - Method in class TraversePointsOnContour
getOutlineWidth() - Method in class BoundingBoxOutline
getOutlineWidth() - Method in class Outline
getOutlineWidth() - Method in class CompareAnnotations: How many pixels should the outline be around objects.
getOutlineWidth() - Method in class AtScale
getOutlineWidth() - Method in class ColoredBase: The width of the outline (only relevant if outline==true.
getOutlineWidth() - Method in class OutlinePreserveRelativeSize: The width of the outline.
getOutlineWidth() - Method in class SegmentInstanceWithModel: The width of the outline.
getOutlineWidth() - Method in class VisualizeOnBackground
getOutlineWidth() - Method in class ExportObjectsAsCroppedImages
getOutPath() - Method in class InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc.
getOutput() - Method in class OutputExperiment: The output-manager that specifies how/where/which elements occur duing outputting.
getOutput() - Method in class ExperimentExecutor
getOutput() - Method in class QuickMultiDatasetExperiment
getOutputDirectory() - Method in class Outputter
getOutputDirectory() - Method in class OutputterChecked
getOutputDirectory() - Method in class OutputPrefixerSettings: A directory indicating where inputs can be located
getOutputEnabledDelta() - Method in class OutputArguments: Additions/subtractions of outputs for the experiment supplied by the user.
getOutputName() - Method in class ToTextFileBase: The name to use (without extension) for the text-file log
getOutputName() - Method in class FeatureCSVMetadata: The output name for the features CSV.
getOutputName() - Method in class OutputtedFile
getOutputName() - Method in class OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
getOutputName() - Method in class PeriodicSubdirectoryReporter
getOutputName() - Method in class MinimalExecutionTimeStatsReporter
getOutputName() - Method in class VoxelizedMarksChangeReporter
getOutputNameStyle() - Method in class OutputPattern
getOutputNameStyle() - Method in class FromOutputName
getOutputPattern() - Method in class BoundOutputter
getOutputRGBOutline() - Method in class ExportObjectsAsCroppedImages
getOutputRGBOutlineFlattened() - Method in class ExportObjectsAsCroppedImages
getOutputsDisabled() - Method in class SpecificDisabled: The names of the outputs that are disbled.
getOutputsEnabled() - Method in class SpecificEnabled: The names of the outputs that are enabled.
getOutputsEnabled() - Method in class OutputManager: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class OutputterChecked: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class ElementOutputter: Which outputs are enabled or not enabled.
getOutputStackProvider() - Method in class ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
getOutputter() - Method in class InitializationContext
getOutputter() - Method in class InputBound
getOutputter() - Method in class InputOutputContextStateful
getOutputter() - Method in class ParametersExperiment
getOutputter() - Method in class BoundOutputter: The outputter to be used for the sequence.
getOutputter() - Method in interface InputOutputContext: An outputter that writes to the particular output-directory.
getOutputter() - Method in class ElementOutputter: The outputter for writing the element.
getOutputter() - Method in class OptimizationContext
getOutputterFor(String) - Method in class SharedStateFilteredImageOutput: groupIdentifierFor should always called at least once before getOutputManagerFor
getOutputWriteSettings() - Method in class OutputManager: General settings (default file extensions, colors etc.) for outtping files.
getOutputWriteSettings() - Method in class QuickExperiment
getOutside() - Method in class UnitsWithinRange: Returned as a constant if a value lies otside the range
getOutsideKernelPolicy() - Method in class KernelApplicationParameters: How to handle voxels that appear in a neighborhood that lies outside the scene boundaries.
getOverlapRatioThreshold() - Method in class KernelBirthAndKill
getOverlays() - Method in class ColoredOverlayCollection
getOverlays() - Method in class IndexableOverlays
getPadding() - Method in class TextStyle: Padding added around the text in both dimensions if a default size is inferred (ignored if an explicit size is specified )
getPadding() - Method in class DrawCroppedObjectsGenerator
getPadding() - Method in class ExportObjectsBase: Padding placed on each side of the outputted image (if it's within the image)
getPaddingXY() - Method in class Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
getPaddingZ() - Method in class Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
getPair() - Method in class MergedPairsFeatures
getPair() - Method in class EnergyPair
getPair() - Method in class MarksWithEnergyBreakdown: Every combination of interactions between marks and the associated energy
getPairAddCriteria() - Method in class EnergySchemeCreatorByElement
getPairAddCriteria() - Method in class EnergyScheme
getPairCollection() - Method in class KernelMerge
getPairsFor(Mark) - Method in class RandomCollectionWithAddCriteria
getPairTypeClass() - Method in class RandomCollectionWithAddCriteria
getParameters() - Method in class EnergyStack: The associated parameters.
getParameters() - Method in class HOGDescriptor: Parameters used for calculating HOG
getParameters() - Method in class HOGFeature: Parameters used for calculating HOG.
getParametersExperiment() - Method in class ParametersUnbound
getParamPrefix() - Method in class PermuteFeatureSequenceInteger
getParent() - Method in class ErrorNodeImpl
getParentDirectory() - Method in class MutableDirectory
getParentDirectory() - Method in class OutputtedFile
getParentDirectoryCreator() - Method in class OutputterTarget
getParentOutputter() - Method in class PeriodicSubdirectoryReporter
getPartition() - Method in class MarksFromPartition
getPath() - Method in class AnnotationWithStrategy: Path to annotation.
getPath() - Method in class NotFound: The path an object was not found at.
getPath() - Method in class RootPath: A path on a file-system to the directory, that defines the root.
getPath() - Method in class SingleFile
getPath() - Method in class NamedFile: The path of NamedFile.getFile().
getPath() - Method in class NamedPath: The path
getPath() - Method in class RootedFilePath
getPath() - Method in class StaticFilePath
getPath() - Method in class FileDetails
getPathAnnotation() - Method in class SinglePathStrategy: Derives the path to the corresponding annotation files, given a path to the image to be annotated.
getPathDefaultMarks() - Method in class MarkProposerStrategy
getPathDictionary() - Method in class MarkProposerStrategy
getPathLabel() - Method in class ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes)
getPathParser() - Method in class GroupFiles
getPaths() - Method in class InputArguments: A list of paths referring to specific inputs;
getPaths() - Method in class FileSetFromStringSet
getPaths() - Method in class FilterForExistingFiles: All files need to be present
getPayload() - Method in class TypedEdge: The edge.
getPayload() - Method in class ObjectVertex
getPenaltyValue() - Method in class MaxOverlapRatio
getPeriodTriggerBank() - Method in class FeedbackBeginParameters
getPermutation() - Method in class PermuteFeature: A permutation to apply.
getPermutations() - Method in class PermuteFeature: A list of permutations to apply.
getPermuteProperty() - Method in class Permute
getPermuteProperty() - Method in class PermuteFeatureSequenceInteger
getPixelsForPlane(int) - Method in class EncodedVoxels
getPlotBackgroundColor() - Method in class PlotColorScheme
getPlotGridlineColor() - Method in class PlotColorScheme
getPlusOne() - Method in class SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index +1 or null if it's the final slice.
getPoint() - Method in class KernelPointCursor: The point around which the cursor may iterate.
getPointFitters() - Method in class PointsInitialization
getPoints() - Method in class PointListBase
getPoints() - Method in class Contour: An ordered list of points in the contour.
getPointsFitter() - Method in class CreateMarkFromPoints
getPointsFitter() - Method in class MarkProposerStrategy: Name of the PointsFitter to use.
getPointsFitter() - Method in class FitPoints
getPointsFitter() - Method in class FitPointsFromObjects
getPointsFitter() - Method in class PointsFitterToMark
getPointsFitter() - Method in class ReflectInAxesWithinDistance
getPointsFromOrientationProposer() - Method in class MergeLists
getPointsFromOrientationXYProposer() - Method in class XYOrientationExtendToZ
getPointsProposer() - Method in class FitPoints
getPosition() - Method in class MarkWithPosition
getPositionProposer() - Method in class Position
getPositionProposer() - Method in class Repeat
getPostcondition() - Method in class DilationContext: If defined, a condition which must be satisfied after an iteration occurs, otherwise no more iterations occur.
getPower() - Method in class MeanRaisedToPower
getPredicates() - Method in class PathMatchConstraints: Predicates for both a file and a directory.
getPrefix() - Method in class DefineAdderWithPrefixBean: A prefix that is placed before the name of every bean created.
getPrefix() - Method in class PrependName: The string to prepend to the custom-name of each feature.
getPrefix() - Method in class PathPrefixerAvoidResolve: A string prefixed to each output-path.
getPrefix() - Method in class OutputterTarget
getPrefix() - Method in class Outputter
getPrefix() - Method in class OutputterChecked
getPrefix() - Method in class DeriveFromPair
getPrefix() - Method in class FeatureListProviderAggregatePair: The string to prepend.
getPrefix() - Method in class ExperimentStructure
getPrefixer() - Method in class OutputArguments: Where outputs are written, and how identifiers are styled.
getPrefixer() - Method in class ParametersExperiment: The OutputManager associated with the experiment which Outputter uses.
getPrefixer() - Method in class OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
getPrefixer() - Method in class PathPrefixerContext: Settings for where and how outputs should be prefixed.
getPrefixer() - Method in class LastDirectoryAsPrefix
getPrefixer() - Method in class Rooted
getPrefixerElse() - Method in class IfIncrementingNumberRequested: Called if the requested condition is not true.
getPrefixerIf() - Method in class IfIncrementingNumberRequested: Called if the requested condition is true.
getPrefixToRemove() - Method in class DirectoryStructure
getPrependColor() - Method in class Prepend: The color to prepend.
getPriority() - Method in class PrioritisedVertex
getProbNeg() - Method in class KernelPosNeg
getProbPos() - Method in class KernelPosNeg
getProgress() - Method in class InputManagerParameters
getProperties() - Method in class ObjectWithProperties: A mapping between keys and corresponding values.
getProperty(String) - Method in class ObjectWithProperties: Retrieves the value of a property corresponding to a particular name.
getPropertyInitializer() - Method in class InitializableBean: Assigns a parameter, if possible, to a bean - as used by bean initializer.
getPropertyPath() - Method in class PermuteProperty: Either a direct property of a bean or a nested-property with the children separated by full-stops.
getProposal() - Method in class OptimizationStep
getProposal() - Method in class Reporting
getProposalSecondary() - Method in class Reporting: An optional additional marks-Energy that provides an additional explanation of proposed
getProposer() - Method in class MarkFromCollectionProposerUnary
getProposer() - Method in class MarkProposerUnary
getProvider() - Method in class FromProvider
getPxlPartMemo() - Method in class FeatureInputAllMemo
getPxlPartMemo() - Method in class FeatureInputSingleMemo
getQuantile() - Method in class Quantile: The quantile.
getQuantile() - Method in class QuantileStretch
getQuantile() - Method in class Quantile
getQuantile() - Method in class DiscardOutliers
getQuantile() - Method in class Quantile
getQuantile() - Method in class QuantileAcrossObjects
getQuantile() - Method in class QuantileAcrossConnectedComponents
getQuantileHigh() - Method in class Range
getQuantileLow() - Method in class Range
getQuantileLower() - Method in class ToByteUpperLowerQuantileIntensity
getQuantileUpper() - Method in class ToByteUpperLowerQuantileIntensity
getRadii() - Method in class Ellipse
getRadii() - Method in class Ellipsoid
getRadiiProposer() - Method in class OrientationAndRadiiProposer
getRadiiProposer() - Method in class RadiiProposerRepeat
getRadius() - Method in class MarkWithPositionAndSingleRadius
getRadius() - Method in class AutoLocalThreshold
getRadius() - Method in class WithRadiusBase
getRadiusBound() - Method in class UniformRandomRadiiProposer
getRadiusX() - Method in class FitResult
getRadiusY() - Method in class FitResult
getRadiusZ() - Method in class FitResult
getRandomNumberGenerator() - Method in class ProposerContext
getRangeAxisLimits() - Method in class PlotInstance
getRangeC() - Method in class SizeExtents
getRangeT() - Method in class SizeExtents
getRangeZ() - Method in class SizeExtents
getRate() - Method in class Geometry
getRaw() - Method in class UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at the current buffer position.
getRaw(int) - Method in class UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at a particular buffer position.
getRaw() - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as an int) at the current buffer position.
getRaw(int) - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as a int) at a particular buffer position.
getRaw() - Method in class UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at the current buffer position.
getRaw(int) - Method in class UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at a particular buffer position.
getReader() - Method in class RotateImageToMatchEXIFOrientation: Reads the image that is subsequently flattened.
getReaderMatching() - Method in class BranchExtension: The reader to use if the extension matches.
getReaderNotMatching() - Method in class BranchExtension: The reader to use if the extension does not match.
getReason() - Method in class NotFound: The reason an object could not be found.
getReceive() - Method in class CombineBase
getRecordedOutputs() - Method in class RecordedOutputsWithRules: If defined, records output-names that are written / not-written during the experiment.
getRed() - Method in class RGBColorBean: The red component value of the RGB color.
getRed() - Method in class RGBColor: The red component value of the RGB color.
getRed() - Method in class ThreeChannels
getReduce() - Method in class FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
getReferencePoissonIntensity() - Method in class MarkWithIdentifierFactory
getReferences() - Method in class ReferencingFeatureListProvider: The names of other feature-lists, whose features may be referenced by this feature.
getReferencesFeatureListCreator() - Method in class PermuteFeature: Makes sure a particular feature list creator is evaluated
getReferencesList() - Method in class FeatureProviderReference: The name of the list in which the feature referenced by id resides.
getRegex() - Method in class RegularExpressionBase
getRegEx() - Method in class RegExMatcher
getRegEx() - Method in class PathRegEx: Regular expression to use to match path with at least one group in it.
getRegEx() - Method in class RemoveMatching: If a path matches a regular expression it is removed.
getRegEx() - Method in class Exclude: A regular-expression to be matched against the identifiers of inputs.
getRegEx() - Method in class InsertRegExGroups: The regular-expression to use for matching groups.
getRegEx() - Method in class JoinRegExGroups
getRegex() - Method in class Replace: Regular expression to match against string
getRegex() - Method in class QuickBase: A regular-expression applied to the image file-path that matches three groups.
getRegEx() - Method in class ExperimentStructure
getRegexAdjacent() - Method in class NamedChannelsQuick: This needs to be set if there is at least one adjacentChannel.
getRegExDir() - Method in class MultiFileReader: If non-empty a regular-expression is applied to directories.
getRegExFile() - Method in class MultiFileReader: If non-empty a regular-expression is applied to files.
getRegion() - Method in class Thresholded
getRegion() - Method in class Intensity
getRegionID() - Method in class RegionMembershipWithFlags
getRegionID() - Method in class VolumeMin
getRegionID() - Method in class FromMarks
getRegionID() - Method in class IndexedRegionBase
getRegionID() - Method in class ColoredMarks
getRegionID() - Method in class FeatureMarkRegion
getRegionID() - Method in class FeatureSingleMemoRegion
getRegionID() - Method in class FeaturePairMemoSingleRegion
getRegionID() - Method in class KernelBirthAndKill
getRegionMap() - Method in class EnergySchemeCreatorByElement
getRegionMap() - Method in class EnergyScheme
getRegionMap() - Method in class EnergySchemeWithSharedFeatures
getRegionMap() - Method in class EnergyMemoList
getRegionMap() - Method in class VoxelizedMarkMemo
getRegionMap() - Method in class ProposerContext
getRegionMap() - Method in class FromMarks
getRegionMap() - Method in class AsObject
getRegionMap() - Method in class SurfaceSizeMaskNonZero
getRegionMembership() - Method in class RegionMembershipWithFlags
getRegularExpression() - Method in class TimestampPattern: The regular-expression that checks a match and specifies groups for the encoded date-time.
getRejectionReason() - Method in class DualMarksAnnotation: A reason for rejection, if the annotation was rejected by the annotator.
getRelation() - Method in class RelationToConstant: The relation to the threshold, where the threshold forms the second operand.
getRelation() - Method in class ObjectFilterRelation
getRelation() - Method in class MergePairs: Relation to threshold
getRelation() - Method in class IdentityImposeValueRelationToHistogram
getRelation() - Method in class RejectIfConditionXYResolution: A predicate defined by the relationship of the XY-resolution to a constant threshold.
getRelation() - Method in class AddCriteriaFeatureRelationThreshold
getRelation() - Method in class RequireFeatureRelationThreshold
getRemainder() - Method in class SplitPath: The second component, what remains in the path.
getRepeat() - Method in class MovieFromSlices
getRepeats() - Method in class KernelBirth: Total number of births
getRepeatZProvider() - Method in class GenerateString: Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider
getReplacement() - Method in class SubstituteRegularExpression
getReplacement() - Method in class Replace: What to replace in the path
getReplacement() - Method in class AdjacentFile: The replacement string used to determine the file
getRequireArguments() - Method in class OnlyIf: The conditions that must be fulfilled
getRequireArguments() - Method in class FeedbackReceiverRequireArguments
getResizeTo() - Method in class GroupedMeanChannelTask: If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
getResizeTo() - Method in class HOGDescriptor: The input-image is rescaled to this width/height before calculating HOG descriptors
getResizeTo() - Method in class HOGFeature: The input is rescaled to this width/height before calculating HOG descriptors.
getResolution() - Method in class BinarySegmentationParameters
getResolutionOptional() - Method in class FeatureInputDimensions
getResolutionOptional() - Method in class FeatureInputEnergy
getResolutionOptional() - Method in interface FeatureInputWithResolution: The resolution of the associated image, if it is available.
getResolutionOptional() - Method in class FeatureInputHistogram
getResolutionOptional() - Method in class FeatureInputMarkCollection
getResolutionOptional() - Method in class FeatureInputMark
getResolutionRequired() - Method in interface FeatureInputWithResolution: The resolution of the associated image, or an exception if it is not available.
getRestrictTo() - Method in class Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
getResult(int) - Method in class ResultsVector: Gets a result value at a particular position.
getResults() - Method in class FeatureInputResults: The results of a prior feature-calculation, corresponding to a list of features.
getResults() - Method in class LabelledResultsVector: The results.
getResults() - Method in class FeatureCalculationContext: The stored results and thumbnail writer.
getResults() - Method in class FeatureExporter: Saved store feature calculation results, and writes associated thumbnails.
getResults() - Method in class LabelledResultsVectorWithThumbnail: The results.
getResultsVector() - Method in class ResultsVectorWithThumbnail
getRGB() - Method in class RGBColorBean: Returns the RGB value encoded as an int as in Color.getRGB().
getRGB() - Method in class RGBColor: Returns the RGB value encoded as an int as in Color.getRGB().
getRgb() - Method in class StackWriteAttributes: Whether it's an RGB or RGBA image when it has three/four channels respectively.
getRight() - Method in class ObjectsToCompare: Objects on right-side of the comparison
getRightUnassigned() - Method in class OverlappingObjects: The unassigned objects in the right set.
getRoot() - Method in class SplitPath: The first component, the root of the path.
getRoot() - Method in class ProposerFailureDescription
getRoot() - Method in class TestLoader: Path to where the test-data is stored.
getRoot1() - Method in class QuadraticEquationSolver.QuadraticRoots: The first root.
getRoot2() - Method in class QuadraticEquationSolver.QuadraticRoots: The second root.
getRootDirectory() - Method in class Manifest
getRootName() - Method in class Rooted: The name of the root-path to associate with this fileset.
getRootName() - Method in class RootedFilePath
getRootName() - Method in class Rooted
getRootName() - Method in class Rooted
getRootName() - Method in class QuickBase: If non-empty then a rooted filesystem is used with this root
getRootName() - Method in class RootedExperiment: Root-name assuming multi-rooted structure.
getRootNameForStructure() - Method in class ExperimentResultsExperimentStructure: If rootInStructure==true, the rootName is placed in the folder structure.
getRootPath() - Method in class DeserializedManifest
getRotationAngle() - Method in class BoundRotation2D
getRotationMatrix() - Method in class Orientation: Derives a RotationMatrix that can be applied to rotate an entity anti-clockwise to the current orientation.
getRotationMatrix() - Method in class OrientationRotationMatrix: The rotation-matrix.
getRotationX() - Method in class BoundRotation3D
getRotationY() - Method in class BoundRotation3D
getRotationZ() - Method in class BoundRotation3D
getRotMatrix() - Method in class FitResult: The rotation matrix, which must be considered immutable to be used here.
getRow(int) - Method in class TableItemArrangement
getRow() - Method in class Cell
getRowForListIndex(int) - Method in class TableItemArrangement
getRunningSum() - Method in class RunningSumParented
getSampleEvery() - Method in class SampleWithDirectory
getScalarProposer() - Method in class MaxWithConstant
getScalarProposer() - Method in class Scale
getScale() - Method in class MeanScale: The scale, typically the standard-deviation.
getScale() - Method in class MontageSlices: Whether to increase or reduce the size of the images
getScaleCalculator() - Method in class ScaleXY
getScaleCalculator() - Method in class ScaleXY: Determines how much to scale by
getScaleCalculator() - Method in class Scale
getScaleCalculator() - Method in class AtScale
getScaleCalculator() - Method in class Invert: The delegate ScaleCalculator whose calculation will be inverted.
getScaleCalculator() - Method in class ScaleImage: Calculates what scale-factor to apply on the image.
getScaleCalculator() - Method in class ScaleXY
getScaleFactor() - Method in class GradientBase
getScaleLower() - Method in class ScaleByDictionary
getScaleLower() - Method in class ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
getScaleRadii() - Method in class ConicFitterBase
getScaleUpper() - Method in class ScaleByDictionary
getScaleUpper() - Method in class ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
getScore() - Method in class ScoreVoxels
getScoreExtracter() - Method in class AcceptanceProbabilityCalculator
getScoreProvider() - Method in class ExtractSlice
getSearchObjects() - Method in class FeatureIntersectingObjects
getSecond() - Method in class CostMatrix: The second set of elements.
getSecond() - Method in class FeatureInputPairObjects
getSecond() - Method in class OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names)
getSecond() - Method in class Compose: Second transformation from U to T
getSecondary() - Method in class StateReporterToPixelized
getSegment() - Method in class BinarySegmentationOne
getSegment() - Method in class SegmentChannelIntoObjectsUnary
getSegment() - Method in class SegmentChannel: Segmentation algorithm
getSegment() - Method in class SegmentChannel
getSegment() - Method in class SegmentChannelByObject
getSegment() - Method in class SegmentStack: The segmentation procedure.
getSegment() - Method in class SegmentWithSeeds
getSegment() - Method in class ConnectedComponentsFromBinarySegmentation
getSegment() - Method in class SegmentInstanceWithModel: The segmentation algorithm.
getSegment() - Method in class SegmentMarksFromImage: How to perform the segmentation.
getSegmentStack() - Method in class SegmentOnMaximumIntensityAndExpandInZ
getSelect() - Method in class DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
getSelectChannels() - Method in class GroupedStackBase: Selects which channels are included, optionally renaming.
getSemiMajorAxis() - Method in class EllipseStandardFormConverter
getSemiMinorAxis() - Method in class EllipseStandardFormConverter
getSeperator() - Method in class CombineCSV
getSequence() - Method in class PermutePropertySequence: A sequence of integers, with each element assigned assigned directly during the permutation, or after further manipulation.
getSequence() - Method in class ChangeableOutputSequence
getSequenceType() - Method in class OutputSequenceIndexed
getSequenceType() - Method in class ManifestDirectoryDescription: A sequence-type to describe the different filenames outputted in the directory.
getSeriesColors() - Method in class PlotIndexBaseCategorical
getSeriesIndex() - Method in class FromStackReader: The series to open to the read the metadata (zero-indexed).
getSeriesNameFor(int) - Method in class PlotIndexBase
getSettings() - Method in class Outputter
getSettings() - Method in class OutputterChecked: General settings for outputting.
getSettings() - Method in class OutputWriteContext: User-define settings for outputting in output-manager.
getSettings() - Method in class ElementOutputter: General settings for outputting.
getSharedFeatures() - Method in class FeatureRelatedInitialization: Shared features available for reference during calculation.
getSharedFeatures() - Method in class EnergySchemeSet
getSharedFeatures() - Method in class EnergySchemeWithSharedFeatures
getSharedObjects() - Method in class FeatureInitialization: Shared-objects, which can be referenced by the feature to influence calculation.
getSharedObjects() - Method in class ImageInitialization
getSharedState() - Method in class InputBound
getSharedState() - Method in class ParametersUnbound
getSharedState() - Method in class CopyContext: State shared across all inputs when copying.
getSharedState() - Method in class SharedStateRememberConverted: The shared state.
getShell() - Method in class MarkEllipseFactory
getShell() - Method in class MarkEllipsoidFactory
getShell() - Method in class Ellipse: The size of the shell, expressed as a ratio of the radius.
getShell() - Method in class Ellipsoid
getShell() - Method in class FromObjects
getShell() - Method in class CreateEllipse
getShell() - Method in class ConicFitterBase
getShortTitle() - Method in class Plot: A shortened version of Plot.getTitle().
getShowOngoingJobsLessThan() - Method in class ParallelProcessor: When the number of ongoing jobs is less than this threshold, they are shown in event logs.
getSigma() - Method in class BlurStrategy
getSigma() - Method in class GaussianBlur2D
getSimplePairCollectionID() - Method in class KernelMerge
getSingle() - Method in class MergedPairsFeatures
getSize() - Method in class TaskArguments: Suggests dimensions or a scaling-factor to resize an image to.
getSize() - Method in class TextStyle: Explicit size of the image the string is draw on
getSize() - Method in class Kernel: The size of the kernel-matrix in one dimension, either X or Y.
getSize() - Method in class Aggregator
getSize() - Method in class PlotHistogram: Size of the image produced showing a plot of the histogram.
getSize() - Method in class OutlinePreserveRelativeSize: Size of all created thumbnails
getSize() - Method in class ScaleToSize
getSize() - Method in class MovieFromSlices
getSize() - Method in class IntegerRange
getSizeXY() - Method in class SpecifyDimensions: Length of X and Y dimensions.
getSizeZ() - Method in class SpecifyDimensions: Length of Z dimension.
getSkipFirstTrim() - Method in class RemoveTrailingDirectory
getSkipFirstTrim() - Method in class FilePathAppendBase
getSkipNumberSubdirectories() - Method in class LastDirectories: Initially skip this number of directories before including them in the description.
getSlice(int) - Method in interface VoxelPartition
getSlice(int) - Method in class VoxelPartitionHistogram
getSlice() - Method in class RepeatSlice
getSliceFirst() - Method in class MontageSlices: First slice.
getSliceID() - Method in class SelectSlicesBase: Index of slice to use, or -1 to use all slices
getSliceIndex() - Method in class RepeatSlice: Which slice to use from mask
getSliceIndex() - Method in class FileDetails
getSliceLast() - Method in class MontageSlices: Last slice.
getSmoothingFactor() - Method in class SplitContourAtSaddlePoints
getSource() - Method in class StringMapItem: The origin of the mapping.
getSource() - Method in class MatchedObject: The source object (which is matched against others)
getSource() - Method in class IdentifiablePair
getSource() - Method in class PairPxlMarkMemo
getSource() - Method in class ExportFeatures: Source of feature-values to be exported.
getSource() - Method in class DualVoxelizedMarks
getSource() - Method in class ToVoxelized
getSourceDirectory() - Method in class CopyContext: Source directory of copying.
getSources() - Method in class MultipleComparer: The other entities to compare with the annotation.
getSplitIdentifierRegex() - Method in class CompareAnnotations: If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.
getSplitProposer() - Method in class KernelSplit
getSquareSize() - Method in class SplitIntoSquares
getStack() - Method in class StackProviderUnary
getStack() - Method in class DisplayStack: The underlying stack that will be displayed, possibly after conversion.
getStack() - Method in class StackProviderWithLabel
getStack() - Method in class ColoredMarksWithDisplayStack
getStack() - Method in class MarksWithDisplayStack
getStack() - Method in class FromStack: Provides a stack.
getStack() - Method in class SegmentStack: The stack to segment
getStack() - Method in class ExportObjectsFromCSV: The stack that is the background for our objects
getStackEnergy() - Method in class FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
getStackEnergy() - Method in class FromImage: Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
getStackEnergy() - Method in class BinaryClassifierImageLabeller
getStackEnergy() - Method in class ExtractSlice
getStackEnergy() - Method in class DefineOutputterWithEnergy
getStackID() - Method in class IfStackExists
getStackName() - Method in class One: If defined, processing only occurs the stack with this specific stack and index.
getStackNameDefault() - Method in class AnnotationBackground: The name of the default stack from backgroundStackMap to display as background when annotating.
getStackProviderID() - Method in class FromStack: Specifies the ID of an existing stack.
getStackProviderID() - Method in class FromStackChannel
getStackReader() - Method in class AnnotatorStrategy: How to read raster Stacks from the file-system.
getStackReader() - Method in class InputManagerWithStackReader
getStackReader() - Method in class MaskAsObject: How to read the Mask from the file-system.
getStackReader() - Method in class AnnotationComparisonInput
getStackReader() - Method in class FromStackReader: The StackReader to use to read the image metadata.
getStackReader() - Method in class FlattenAsChannel: Reads the image that is subsequently flattened.
getStackReader() - Method in class ImposeResolution: Reads an image before a resolution is imposed.
getStackReader() - Method in class MultiFileReader
getStackReader() - Method in class ReadVoxelExtentXml: Reads an image before a resolution is imposed.
getStackReader() - Method in class RejectIfConditionXYResolution: Reads an image before a resolution is imposed.
getStackReaderAdjacent() - Method in class NamedChannelsQuick: The raster-reader to use for opening any adjacent-channels
getStackReaderAppend() - Method in class QuickBase: The raster-reader for reading any appended files
getStackStore() - Method in class ChannelSource
getStart() - Method in class SequenceInteger: The index to begin iteration from.
getStartIndex() - Method in class IndexRangeNegative: The index if the first element to use in the subsetting range, zero-indexed.
getStartIndex() - Method in class MovieFromSlices
getStartingIntensity() - Method in class FloodFillEachIntensityLevel: The first intensity-value to consider as a valid object (e.g.
getStartPoint() - Method in class LineSegment
getState() - Method in class FeedbackEndParameters
getStateReporter() - Method in class TransformationAssignMode
getStrategy() - Method in class AnnotationWithStrategy: The strategy on how annotation occurs.
getStrategy() - Method in class BoundReplaceStrategy
getStrategy() - Method in class Blur
getStringRasterGenerator() - Method in class GenerateString
getStyle() - Method in class ExportFeatures: Visual style for how feature export occurs.
getStyle() - Method in class SegmentInstanceWithModel: Visual style for how feature export occurs.
getSubdirectory() - Method in class AppendDictionary
getSubdirectory() - Method in class ExperimentResultsExperimentStructure: If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
getSubdirectoryName() - Method in class OutputPattern: The name of a subdirectory in the current context to write to, or if empty, files are written into the current directory context.
getSubtractConstant() - Method in class IntensityGradientBase
getSubtractRadii() - Method in class ConicFitterBase
getSuggestedFormatToWrite() - Method in class StackWriteOptions: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class OutputWriteContext: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class ElementOutputter
getSuggestedImageOutputFormat() - Method in class OutputPrefixerSettings: A file format suggested for writing images to the file system.
getSuggestedResize() - Method in class InitializationContext: A suggested input on how to resize an image, if one is provided.
getSuggestedResize() - Method in class ImageInitialization
getSum() - Method in class RunningSum: The running sum.
getSummarizer() - Method in class SummarizerInputFromManager
getSummarizer() - Method in class SummarizeBase
getSummarizerElse() - Method in class SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
getSummarizerGreaterThan() - Method in class SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
getTarget() - Method in class StringMapItem: The destination of the mapping.
getTargetClass() - Method in class ExtractDerivedParameter: The class of the target type T.
getTargetSize() - Method in class FitTo: The target size.
getTask() - Method in class JobProcessor
getTask() - Method in class ExperimentExecutor
getTask() - Method in class ConvertNamedChannels: The underlying task that will be called, perhaps with a different input-type.
getTask() - Method in class QuickExperiment
getTask() - Method in class QuickMultiDatasetExperiment
getTask() - Method in class QuickMultiDatasetStructuredExperiment
getTaskArguments() - Method in class InputBound
getTaskName() - Method in class TaskArguments: A name to describe the ongoing task.
getTaskProcessor() - Method in class InputOutputExperiment: What task is associated with the experiment, and how it is processed.
getTemperature() - Method in class Aggregator
getTemperature() - Method in class Reporting
getTemplateMark() - Method in class MarkWithIdentifierFactory
getTemporary() - Method in class EncodedVoxels
getTermination() - Method in class SimulatedAnnealing
getText() - Method in class GenerateString: Text to draw on an image
getThreshold() - Method in class RelationToConstant: The constant threshold.
getThreshold() - Method in class CutBelowThreshold
getThreshold() - Method in class CalculateLevelRelativeToThreshold
getThreshold() - Method in class IntensityGreaterEqualThan
getThreshold() - Method in class ThresholdedFeature
getThreshold() - Method in class ThresholdedVolume
getThreshold() - Method in class Count
getThreshold() - Method in class RatioThreshold
getThreshold() - Method in class FeatureIntersectingObjectsThreshold: Only considers values greater or equal to the threshold
getThreshold() - Method in class AddCriteriaFeatureRelationThreshold
getThreshold() - Method in class RequireFeatureRelationThreshold
getThreshold() - Method in class GreatestAreaSlice
getThreshold() - Method in class Thresholded
getThreshold() - Method in class IfCondition
getThresholder() - Method in class BinarySegmentationThreshold
getThresholder() - Method in class Threshold: The thresholder that will convert a channel into a binary-channel
getThresholdHours() - Method in class ClusterByTimestamp: Files whose creation-time differs <= this parameter are joined into the same cluster.
getThresholdNumberObjectsGlobal() - Method in class ThresholdConfidence: When the number of objects is greater or equal than this, they are reduced globally, without separation.
getThumbnail() - Method in class CombineObjectsForFeatures: Generates a thumbnail representation of one or more combined objects, as form a single input.
getThumbnail() - Method in class FromImage: Method to generate a thumbnail for images.
getThumbnail() - Method in class ResultsVectorWithThumbnail
getThumbnailBatch() - Method in class ListWithThumbnails
getTime() - Method in class JobState
getTimeAnnotationLastUpdated() - Method in class DualMarksAnnotation: Number of seconds since the UNIX epoch
getTimeIndex() - Method in class ConvertNamedChannelsToStack
getTimeIndex() - Method in class FileDetails
getTimeIndexGroupID() - Method in class RegularExpression
getTimes() - Method in class Repeat: How many times to duplicate the list.
getTimestampPatterns() - Method in class ClusterByTimestamp: The patterns which can be used to extract a date-time from a filename.
getTimeZoneOffset() - Method in class ClusterByTimestamp: If >= 0, sets a specific time-offset in hours.
getTitle() - Method in class ReportFeatureEvaluator
getTitle() - Method in class Plot: The full title of the plot.
getTitle() - Method in class ReportFeatureForManifestFileBase
getTo() - Method in class TypedEdge: The vertex the edge joins to.
getTolerance() - Method in class UnchangedScore: An exponent of 10 which determines a tolerance, less than which a score will be deemed unchanged compared to another.
getTotal() - Method in class EnergyTotal
getTotalCount() - Method in class Histogram: The total count across values in the histogram.
getTotalNumberTasks() - Method in class ConcurrentJobMonitor
getTransformer() - Method in class RemovePartitionAndThen
getTransformer() - Method in class VoxelizeWithTransform
getTransformer() - Method in class KernelStateBridgePixelize
getTransformerKernelToState() - Method in class KernelStateBridgeTransformer
getTransformerMarks() - Method in class AddDualTransformer
getTransformerPrimary() - Method in class StateReporterTransformer
getTransformerSecondary() - Method in class StateReporterTransformer
getTransformerStateToKernel() - Method in class KernelStateBridgeTransformer
getTriggerTerminationCondition() - Method in class OptimizationContext
getTrimTrailingDirectory() - Method in class RemoveTrailingDirectory
getTrimTrailingDirectory() - Method in class FilePathAppendBase
getType() - Method in class ManifestDescription: Identifies the type of entity.
getUnconvertedVoxelAt(int, Point3i) - Method in class DisplayStack: Retrieve the intensity of a voxel at a particular point, before any conversion is applied.
getUniqueLabel() - Method in class AnnotationLabel: Label that uniquely identifies the ID (for machine purposes)
getUnit() - Method in class BoundingBoxExtent
getUnit() - Method in class FeatureSingleMemoRegion
getUnitConverterOptional() - Method in class FeatureInputEnergy: Converts voxelized measurements to/from physical units.
getUnitType() - Method in class DistancePhysical
getUnitType() - Method in class AreaPhysical
getUnitType() - Method in class VolumePhysical
getUnitType() - Method in class FeatureConvertUnits
getUnitType() - Method in class UnitConverter
getUnitTypeFrom() - Method in class ConvertUnits
getUnitTypeTo() - Method in class ConvertUnits
getUnitValueDistance() - Method in class FromUnitValueDistance
getUnsigned() - Method in class UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at the current buffer position.
getUnsigned(int) - Method in class UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at a particular buffer position.
getUnsigned() - Method in class UnsignedByteBuffer
getUnsigned(int) - Method in class UnsignedByteBuffer
getUnsigned() - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at the current buffer position.
getUnsigned(int) - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at a particular buffer position.
getUnsigned() - Method in class UnsignedShortBuffer
getUnsigned(int) - Method in class UnsignedShortBuffer
getUnsignedByte() - Static method in class VoxelsFactory: A factory that creates voxels of type unsigned byte.
getUnsignedInt() - Static method in class VoxelsFactory: A factory that creates voxels of type unsigned int.
getUnsignedShort() - Static method in class VoxelsFactory: A factory that creates voxels of type unsigned short.
getUserFriendlyLabel() - Method in class AnnotationLabel: Descriptive user-friendly label displayed via GUI
getValue() - Method in class NamedBean
getValue() - Method in interface NameValue: The associated value.
getValue() - Method in class SimpleNameValue
getValue() - Method in class TypedValue: The value.
getValue() - Method in class Constant: The constant value.
getValue() - Method in class DistancePhysical
getValue() - Method in class DistanceVoxels
getValue() - Method in class UnitValueArea
getValue() - Method in class VolumePhysical
getValue() - Method in class VolumeVoxels
getValue() - Method in class OptionalNameValue: The value.
getValue() - Method in class AssignValue
getValue() - Method in class CreateNew
getValue() - Method in class UnaryWithValueBase
getValue() - Method in class DictionaryCondition: The value the key should have in the dictionary, in order for the condition to be fulfilled.
getValue() - Method in class EmptyHistogramConstant
getValue() - Method in class IfParamEqual
getValue() - Method in class ConstantScaleFactor
getValue() - Method in class CountEqual
getValue() - Method in class IdentityImposeValueRelationToHistogram
getValue() - Method in class NormalizeByConstant
getValue() - Method in class Constant
getValue() - Method in class Constant
getValue() - Method in class WithValueBase
getValueIfEmpty() - Method in class FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false.
getValueIfTooFewVoxels() - Method in class ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments
getValueNoObject() - Method in class ScoreObjects
getValueNoObjects() - Method in class FeatureIntersectingObjects
getValues() - Method in class StatisticsToExport: The values of statistics describing the annotation-comparison, corresponding exactly to the names in StatisticsToExport.getNames().
getValues() - Method in class PermutePropertyDoubleSet: The respect double values to assign during the permutation.
getValues() - Method in class PermutePropertyStringSet: The respect string values to assign during the permutation.
getVersion() - Method in class ExperimentIdentifierConstant
getVertex() - Method in class PrioritisedVertex
getVerticalAlign() - Method in class Overlay
getVisitScheduler() - Method in class TraverseOuterContourOnImage
getVoxelDataType() - Method in class Channel: The underlying data-type of the voxels in the channel, represented by a VoxelDataType instance.
getVoxelDataType() - Method in class VoxelsUntyped: The underlying data-type of the voxels, represented by a VoxelDataType instance.
getVoxels() - Method in class SlidingBuffer: The voxels from which buffers corresponding to slices are extracted.
getVoxelsConverter() - Method in class MaxIntensity
getVoxelsConverter() - Method in interface ChannelConverterAttached: Converts voxels to have type voxel-type T.
getVoxelsConverter() - Method in class MaxIntensityFromHistogram
getVoxelsConverter() - Method in class QuantileIntensityFromHistogram
getVoxelsConverter() - Method in class UpperLowerQuantileIntensityFromHistogram
getVoxelsConverter() - Method in class ChannelConverter: A converter used to change the Voxels to targetDataType.
getWeight() - Method in class WeightedKernel
getWeight() - Method in class KernelProposerOptionSingle
getWeightBackground() - Method in class OtsuWeighted
getWeightedKernelFactory(int) - Method in class KernelProposer
getWeightForeground() - Method in class OtsuWeighted
getWeightItem1Greater() - Method in class Range
getWeightItem2Greater() - Method in class Range
getWeightNegative() - Method in class KernelProposerOption
getWeightNegative() - Method in class KernelProposerOptionDual
getWeightNegative() - Method in class KernelProposerOptionSingle
getWeightPositive() - Method in class KernelProposerOption
getWeightPositive() - Method in class KernelProposerOptionDual
getWeightPositive() - Method in class KernelProposerOptionSingle
getWeightWidthDescription() - Method in class ImageLabelStrategy
getWhenBinaryChannel() - Method in class BranchChannels: Writer employed if a stack is a single-channeled binary image.
getWhenDetailed() - Method in class SwitchDetailedLogging: Logger to use when detailed-logging is on
getWhenEqual() - Method in class IfParamEqual
getWhenFalse() - Method in class IfElse
getWhenNot() - Method in class SwitchDetailedLogging: Logger to use when detailed-logging is off
getWhenNotEightBit() - Method in class BranchChannels: Writer employed if a stack contains channels that are not 8-bit.
getWhenNotEqual() - Method in class IfParamEqual
getWhenRelative() - Method in class IfRelativeToDirectory: The namer to use if the relative-to-directory option is selected.
getWhenRGB() - Method in class BranchChannels: Writer employed if a stack is a three-channeled RGB image.
getWhenRGBAlpha() - Method in class BranchChannels: Writer employed if a stack is a four-channeled RGBA image.
getWhenSingleChannel() - Method in class BranchChannels: Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
getWhenThreeChannels() - Method in class BranchChannels: Writer employed if a stack is a three-channeled non-RGB image.
getWhenTrue() - Method in class IfElse
getWidth() - Method in class SizeXY: Size in X dimension.
getWidth() - Method in class Difference: Width (what the difference is divided by)
getWidth() - Method in class ImposeResolution: Physical pixel size of a voxel in x-dimension.
getWidthFactor() - Method in class DifferenceCalculateLevelStandardDeviation
getWindowSize() - Method in class CenterSliceWindow
getWindowSize() - Method in class HOGParameters: The window-size as per OpenCV implementation.
getWithin() - Method in class UnitsWithinRange: Returned as a constant if a value lies within the range
getWithinValue() - Method in class CompareWithRange: Constant to return if value lies within the range
getWithinValue() - Method in class CompareWithRangeFeature: Constant to return if value lies within the range
getWriter() - Method in class Flatten
getWriter() - Method in class TextFileOutput
getWriter() - Method in class BranchChannels: Default writer, if a more specific writer is not specified for a condition.
getWriter() - Method in class WriteResolutionXml
getWriterAlways2D() - Method in class BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
getWriterElse() - Method in class BranchStack: Otherwise the writer to use.
getWriterIfNoSuggestion() - Method in class BranchSuggestedFormat: The writer to use if there is no suggested file-format.
getWriterInstance(Class<? extends T>) - Method in class OutputWriteSettings: Gets a writer-instance for a particular writerParentClass.
getWriters() - Method in class OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
getWriters() - Method in class OutputterChecked: The writers associated with this output-manager.
getWritersIfSuggested() - Method in class BranchSuggestedFormat: A list of writers to select if a given format is used
getX() - Method in class VectorInDirection
getX() - Method in class PlotAxisLabels
getXDiv() - Method in class Orientation
getXmlAggregatedGroup() - Method in class FeatureOutputNames: The name of the XML file outputted with aggregated values for each group, if enabled.
getXMLConfiguration() - Method in class Experiment
getY() - Method in class VectorInDirection
getY() - Method in class PlotAxisLabels
getYAxisLowerMargin() - Method in class LinePlot
getYAxisUpperMargin() - Method in class LinePlot
getYVal(T, int) - Method in interface LinePlot.YValGetter
getYValGetter() - Method in class BarPlot
getYValGetter() - Method in class LinePlot
getZ() - Method in class VectorInDirection
getZAlign() - Method in class Overlay
getZSliceGroupID() - Method in class RegularExpression
getZSliceNum() - Method in class SortedSetSlice
GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
GlobExtractor - Class in org.anchoranalysis.io.input.path: Extracts a glob from a string describing it, and a direcory which gives it context.
GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path
GlobWithDirectory(Optional<String>, String) - Constructor for class GlobExtractor.GlobWithDirectory
GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Base class to calculate the gradient of the voxels in a Channel.
GradientBase() - Constructor for class GradientBase
GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Like GradientBase but allows an arbitrary constant to be added to voxels storing the gradient.
GradientBaseAddSum() - Constructor for class GradientBaseAddSum
gradientCalculation() - Method in class IntensityGradientBase
GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Extracts the gradient in the direction of a particular axis (identified by an index)
GradientForAxis() - Constructor for class GradientForAxis
GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMagnitude() - Constructor for class GradientMagnitude
GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMeanForAxis() - Constructor for class GradientMeanForAxis
GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Calculates a Channel's gradient along the x and y axes.
GradientXY() - Constructor for class GradientXY
GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
GraphLogger(DescribeGraph, Logger) - Constructor for class GraphLogger
GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, where edges contain no payload.
GraphWithoutPayload(boolean) - Constructor for class GraphWithoutPayload: Creates the graph.
GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, with edges containing a payload of type E.
GraphWithPayload(boolean) - Constructor for class GraphWithPayload: Creates the graph.
GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
GrayscaleReconstruction2DIJ() - Constructor for class GrayscaleReconstruction2DIJ
GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
GrayscaleReconstructionByErosion() - Constructor for class GrayscaleReconstructionByErosion
GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
GrayscaleReconstructionRobinson() - Constructor for class GrayscaleReconstructionRobinson
GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
GreaterIntersectionWith() - Constructor for class GreaterIntersectionWith
GreaterThan - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is greater than valueSecond.
GreaterThan() - Constructor for class GreaterThan
GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 > double2.
GreaterThanBean() - Constructor for class GreaterThanBean
GreaterThanEqualTo - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is greater than or equal to valueSecond.
GreaterThanEqualTo() - Constructor for class GreaterThanEqualTo
GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 >= double2.
GreaterThanEqualToBean() - Constructor for class GreaterThanEqualToBean
GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
GreaterThanThreshold() - Constructor for class GreaterThanThreshold
GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
GreatestAreaSlice() - Constructor for class GreatestAreaSlice
greedyMatch() - Method in class HungarianAlgorithm: Find a valid matching by greedily selecting among zero-cost matchings.
GREEN - Static variable in class RGBChannelNames: Name for the green channel.
green() - Method in class RGBStack: The green channel.
GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label: A set of annotation labels partitoned into their unique groups
GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class GroupedAnnotationLabels
groupedLabels() - Method in class ImageLabelStrategy
GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster: Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value across the group.
GroupedMeanChannelTask() - Constructor for class GroupedMeanChannelTask
GroupedResults - Class in org.anchoranalysis.feature.io.results.group: Stores feature-calculation results, indexing by their group.
GroupedResults() - Constructor for class GroupedResults
GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Commonality between shared state for gouped export tasks
GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class GroupedSharedState
GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped: Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupedStackBase() - Constructor for class GroupedStackBase
GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group: An InputManagerWithStackReader that can unify separate images in separate files to form a single Stack.
GroupFiles() - Constructor for class GroupFiles
groupForKey(String) - Method in class AnnotationComparisonAssigner
groupForKey(String) - Method in class FeatureCostAssigner
groupForKey(String) - Method in class MaskIntersectionAssigner
GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a set of definitions of classes can be collectively grouped using this class.
GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
GroupMapByName(String, String, Supplier<T>) - Constructor for class GroupMapByName: Creates a group-map.
groupNameSet() - Method in class IndexedCSVRows
groupsForImage(SplitString) - Method in class ComparisonSharedState
growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels: Grows the voxel buffer in the positive and negative directions by a certain amount.
growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class ObjectMask: Grows the object-mask's voxel buffers in the positive and negative directions by a certain amount.
growBy(Tuple3i, Extent) - Method in class BoundingBox: Grow the bounding-box by toAdd amount in each dimension in both positive and negative directions.
growBy(int) - Method in class Extent: Creates a new Extent with toAdd size added to each dimension.
growBy(ReadableTuple3i) - Method in class Extent: Creates a new Extent with toAdd size added to each respective dimension.
growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels: Grows a single z-sliced BoundedVoxels by duplicating the slice across the z-dimension sizeZ number of times.
growToZ(int) - Method in class ObjectMask: Grows a single z-sliced ObjectMask by duplicating the slice across the z-dimension sizeZ number of times.
guaranteedImageAttributes() - Method in class AssignmentGenerator
guaranteedImageAttributes() - Method in class ChannelGenerator
guaranteedImageAttributes() - Method in class ObjectsAsGrayscaleGenerator
guaranteedImageAttributes() - Method in class ObjectAsMaskGenerator
guaranteedImageAttributes() - Method in class ObjectsAsRGBGenerator
guaranteedImageAttributes() - Method in class DrawObjectOnStackGenerator
guaranteedImageAttributes() - Method in class ExtractBoundingBoxAreaFromStackGenerator
guaranteedImageAttributes() - Method in class DisplayStackGenerator
guaranteedImageAttributes() - Method in class FlattenStackGenerator
guaranteedImageAttributes() - Method in class RasterGenerator: Guarantees on the attributes of all images created by the generator.
guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToDisplayStack
guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToRaster
guaranteedImageAttributes() - Method in class StackGenerator
guaranteedImageAttributes() - Method in class MarksAsUniqueValueGenerator
guaranteedImageAttributes() - Method in class MarksGeneratorBase
GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Guesses dimensions from an input-image if it exists.
GuessDimensions() - Constructor for class GuessDimensions

H

has(K) - Method in class LRUCache: Is a particular key present already in the cache?
hasAllRequiredArguments(boolean) - Method in class RequireArguments
hasAllRequiredArguments(boolean) - Method in class RequireDebugMode
hasArray() - Method in class UnsignedBuffer: Whether the buffer has an array?
hasAtLeastOneDisabled() - Method in class MultiLevelRecordedOutputs: If there is at least one disabled output.
hasAtLeastOneDisabled() - Method in class RecordedOutputs: If there is at least one disabled output.
hasAtLeastOneEnabled() - Method in class RecordedOutputs: If there is at least one enabled output.
hasAtLeastOneMultiplex(boolean) - Method in class RecordedOutputs: Multiplex between RecordedOutputs.hasAtLeastOneEnabled() and RecordedOutputs.hasAtLeastOneDisabled().
hasBeenInit() - Method in class KernelReplace
hasBeenInitialized() - Method in class OutputWriteSettings
hasCachedResult() - Method in class CalculationPart: Has the calculation already been executed, with a cached result existing?
hasChannel(String) - Method in class ChannelFilter
hasChannel(String) - Method in interface ChannelGetter
hasChannel(String, Logger) - Method in class NamedChannelsInputPart
hasChannel(String) - Method in class NamedChannelsForSeriesConcatenate
hasChannel(String) - Method in class NamedChannelsForSeriesMap
hasChannel(String) - Method in class ChannelGetterForTimepoint
hasColorGetter() - Method in class PlotIndexBaseCategorical
HasFriendlyErrorMessage - Interface in org.anchoranalysis.core.exception.friendly: Methods for extracting a user-friendly error description.
hashCode() - Method in class ImageLabelAnnotation
hashCode() - Method in class CostMatrix
hashCode() - Method in class Found
hashCode() - Method in class NotFound
hashCode() - Method in interface GenerateUniqueParameterization
hashCode() - Method in class DoubleList
hashCode() - Method in class DoubleSet
hashCode() - Method in class IntegerList
hashCode() - Method in class IntegerSet
hashCode() - Method in class StringList
hashCode() - Method in class StringSet
hashCode() - Method in class RootPath
hashCode() - Method in class EqualToBean
hashCode() - Method in class GreaterThanBean
hashCode() - Method in class GreaterThanEqualToBean
hashCode() - Method in class LessThanBean
hashCode() - Method in class LessThanEqualToBean
hashCode() - Method in class RelationBean
hashCode() - Method in class RelationToConstant
hashCode() - Method in class RGBColor
hashCode() - Method in class TypedEdge
hashCode() - Method in class Indexable
hashCode() - Method in class IndexRangeNegative
hashCode() - Method in class CommonContext
hashCode() - Method in class TraversalResult
hashCode() - Method in class FilenameSplitExtension
hashCode() - Method in class SplitPath
hashCode() - Method in class TypedValue
hashCode() - Method in class ParametersUnbound
hashCode() - Method in class RunningSumParented
hashCode() - Method in class ChildCacheName
hashCode() - Method in class ResolvedPart
hashCode() - Method in class ResolvedPartMap
hashCode() - Method in class CalculationPart
hashCode() - Method in class CalculationPartMap
hashCode() - Method in class FeatureInitialization
hashCode() - Method in class FeatureInputDimensions
hashCode() - Method in class FeatureInputEnergy
hashCode() - Method in class FeatureInputNull
hashCode() - Method in class FeatureInputResults
hashCode() - Method in class FeatureCSVMetadata
hashCode() - Method in class CombinedName
hashCode() - Method in class SimpleName
hashCode() - Method in class LabelledResultsVector
hashCode() - Method in class ResultsVector
hashCode() - Method in class BoundingBoxesOnPlane
hashCode() - Method in class SizeXY
hashCode() - Method in class CalculateLevel
hashCode() - Method in class CalculateLevelOne
hashCode() - Method in class BinaryNotOffVoxels
hashCode() - Method in class BinaryNotOnVoxels
hashCode() - Method in class BinaryOffVoxels
hashCode() - Method in class BinaryOnVoxels
hashCode() - Method in class BinaryVoxelsBase
hashCode() - Method in class Dimensions
hashCode() - Method in class Resolution
hashCode() - Method in class Mask
hashCode() - Method in class OverlappingObject
hashCode() - Method in class MatchedObject
hashCode() - Method in class ObjectWithProperties
hashCode() - Method in class Stack
hashCode() - Method in class CalculateInputFromPair
hashCode() - Method in class CalculateNumberVoxels
hashCode() - Method in class NamedFeatureCalculatorMulti
hashCode() - Method in class FeatureInputImageMetadata
hashCode() - Method in class FeatureInputObjectCollection
hashCode() - Method in class FeatureInputPairObjects
hashCode() - Method in class FeatureInputSingleObject
hashCode() - Method in class FeatureInputStack
hashCode() - Method in class ImageTimestampsAttributes
hashCode() - Method in class BinaryValuesByte
hashCode() - Method in class BinaryValuesInt
hashCode() - Method in class UnsignedBuffer
hashCode() - Method in class UnsignedBufferAsInt
hashCode() - Method in class UnsignedByteBuffer
hashCode() - Method in class UnsignedIntBuffer
hashCode() - Method in class UnsignedShortBuffer
hashCode() - Method in class VoxelDataType
hashCode() - Method in class KernelApplicationParameters
hashCode() - Method in class ObjectCollection
hashCode() - Method in class ImageFileEncoding
hashCode() - Method in class ImageFileShape
hashCode() - Method in class OptionalNameValue
hashCode() - Method in class BoundOutputter
hashCode() - Method in class FileNamerContext
hashCode() - Method in class NamedFile
hashCode() - Method in class InputsWithDirectory
hashCode() - Method in class GlobExtractor.GlobWithDirectory
hashCode() - Method in class DualPathPredicates
hashCode() - Method in class PathMatchConstraints
hashCode() - Method in class FileType
hashCode() - Method in class ManifestDescription
hashCode() - Method in class OutputterTarget
hashCode() - Method in class Outputter
hashCode() - Method in class NamedPath
hashCode() - Method in class HelpConfig
hashCode() - Method in class QuadraticEquationSolver.QuadraticRoots
hashCode() - Method in class MeanScale
hashCode() - Method in class EigenvalueAndVector
hashCode() - Method in class RegionMap
hashCode() - Method in class RegionMembership
hashCode() - Method in class RegionMembershipWithFlags
hashCode() - Method in class CalculateDeriveSingleMemoFromPair
hashCode() - Method in class FeatureInputMark
hashCode() - Method in class EnergyPair
hashCode() - Method in class IndexableMarksWithEnergy
hashCode() - Method in class FeatureInputAllMemo
hashCode() - Method in class FeatureInputPairMemo
hashCode() - Method in class FeatureInputSingleMemo
hashCode() - Method in class MemoList
hashCode() - Method in class ColoredMarksWithDisplayStack
hashCode() - Method in class MarksWithDisplayStack
hashCode() - Method in class OverlayMark
hashCode() - Method in class IdentifiablePair
hashCode() - Method in class PairPxlMarkMemo
hashCode() - Method in class ProposerContext
hashCode() - Method in class DualStack
hashCode() - Method in class FeedbackBeginParameters
hashCode() - Method in class FeedbackEndParameters
hashCode() - Method in class KernelWithIdentifier
hashCode() - Method in class IndexableOverlays
hashCode() - Method in class OverlayObjectMask
hashCode() - Method in class Overlay
hashCode() - Method in class ObjectDrawAttributes
hashCode() - Method in class AxisLimits
hashCode() - Method in class ObjectsToCompare
hashCode() - Method in class CalculateLevelListBase
hashCode() - Method in class CalculateLevelRelativeToThreshold
hashCode() - Method in class ClampHistogramMax
hashCode() - Method in class Constant
hashCode() - Method in class EmptyHistogramConstant
hashCode() - Method in class IfGreaterThan
hashCode() - Method in class IfLessThan
hashCode() - Method in class Maximum
hashCode() - Method in class Minimum
hashCode() - Method in class Otsu
hashCode() - Method in class OtsuWeighted
hashCode() - Method in class Quantile
hashCode() - Method in class MorphologicalIterations
hashCode() - Method in class CalculateIntersecting
hashCode() - Method in class CalculateDeriveObjectInput
hashCode() - Method in class CalculateInputFromDelegate
hashCode() - Method in class CalculateInputFromDelegateOption
hashCode() - Method in class CalculateIncrementalOperationMap
hashCode() - Method in class CalculateObjectMask
hashCode() - Method in class CalculateShellObjectMask
hashCode() - Method in class CalculateDilation
hashCode() - Method in class CalculateDilationMap
hashCode() - Method in class CalculateErosion
hashCode() - Method in class CalculateErosionMap
hashCode() - Method in class CalculateHistogram
hashCode() - Method in class CalculateHistogramMasked
hashCode() - Method in class ChangeableOutputSequence
hashCode() - Method in class FeatureExporterContext
hashCode() - Method in class InitializationWithEnergyStack
hashCode() - Method in class LabelledResultsVectorWithThumbnail
hashCode() - Method in class ResultsVectorWithThumbnail
hashCode() - Method in class NamedChannel
hashCode() - Method in class ImageCSVLabellerInitialization
hashCode() - Method in class ImageLabellerStringMapInitialization
hashCode() - Method in class CopyContext
hashCode() - Method in class FileDetails
hashCode() - Method in class SortedSetChannel
hashCode() - Method in class SortedSetSlice
hashCode() - Method in class AnonymizeSharedState
hashCode() - Method in class AllSlicesMaskEverythingNonZero
hashCode() - Method in class AllSlicesMaskNonZero
hashCode() - Method in class CenterSlice
hashCode() - Method in class CenterSliceBase
hashCode() - Method in class CenterSliceWindow
hashCode() - Method in class GreatestAreaSlice
hashCode() - Method in class IndexedRegionBase
hashCode() - Method in class SelectSlicesBase
hashCode() - Method in class SelectSlicesWithIndexBase
hashCode() - Method in class Specific
hashCode() - Method in class DistanceIndex
hashCode() - Method in class DistanceIndexTwice
hashCode() - Method in class ConvertedInput
hashCode() - Method in class CalculateDeriveMarkCollectionInput
hashCode() - Method in class CalculateDeriveMarkInput
hashCode() - Method in class CalculateOverlap
hashCode() - Method in class CalculateOverlapMask
hashCode() - Method in class CalculateOverlapMIP
hashCode() - Method in class CalculateOverlapMIPBase
hashCode() - Method in class CalculateOverlapMIPRatio
hashCode() - Method in class KernelDeath.MarkAnd
hashCode() - Method in class ToVoxelized
hashCode() - Method in class HOGParameters
hashCode() - Method in class FitResult
hashCode() - Method in class CalculateEllipseLeastSquares
hashCode() - Method in class ObjectWithEllipse
hashCode() - Method in class CalculateEllipsoidLeastSquares
hashCode() - Method in class BoundingBox
hashCode() - Method in class Extent
hashCode() - Method in class Orientation
hashCode() - Method in class Orientation2D
hashCode() - Method in class Orientation3DEulerAngles
hashCode() - Method in class OrientationAxisAngle
hashCode() - Method in class OrientationRotationMatrix
hashCode() - Method in class Point2d
hashCode() - Method in class Point2f
hashCode() - Method in class Point2i
hashCode() - Method in class Point3d
hashCode() - Method in class Point3f
hashCode() - Method in class Point3i
hashCode() - Method in class Tuple3d
hashCode() - Method in class Tuple3f
hashCode() - Method in class Tuple3i
hashCode() - Method in class Vector3d
hashCode() - Method in class ScaleFactor
hasHdf5Extension(Path) - Static method in class ObjectCollectionReader
hasHeaders() - Method in class CSVReader.OpenedCSVFile
hasIdenticalXY() - Method in class ScaleFactor: Is the scale-factor identical in X and Y dimensions?
hasIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class CountVoxelsIntersectingObjects: Determines whether there are any intersecting voxels on two object-masks.
hasIntersectingVoxels(ObjectMask) - Method in class ObjectMask: Determines whether there are any intersecting voxels on two object-masks.
hasKey(U) - Method in class CalculationPartMap: Does a result exist for the current input, and a particular key?
hasLastDivider() - Method in class Aggregator
hasMatch(String) - Method in class RegEx: Returns a boolean whether the regular-expression successfully matches a string or not.
hasMoreThanOneSlice() - Method in class Stack: Does the stack have more than one slice in the z-dimension?
hasNecessaryExtents() - Method in class SizeExtents
hasNext() - Method in interface TableItemArrangement.TableCreator
hasNext() - Method in class PriorityQueueIndexRangeDownhill
hasNoCombinableNestedExceptions() - Method in exception AnchorCombinableException: Are there nested-exceptions (according to our traversal rules) that are combinable?
hasNonZeroCount(int) - Method in class Histogram: Whether at least one value, greater or equal to startMin has non-zero count?
hasOffVoxel() - Method in class BinaryVoxels: At least one voxel exists with an off value.
hasOneSlice() - Method in class EnergyStack: Does exactly one z-slice exist in the energy stack?
hasOnVoxel() - Method in class BinaryVoxels: At least one voxel exists with an on value.
hasOption(String) - Method in class CommandLineExtracter: Identical to CommandLine.hasOption(java.lang.String).
hasOptionWithoutArgument(String) - Method in class CommandLineExtracter: Checks if an option exists, but without any argument(s) specified.
hasProperty(String) - Method in class ObjectWithProperties: Whether a particular property exists with a particular name.
hasRemaining() - Method in class UnsignedBuffer: Whether there are elements between the current position and the limit Buffer.hasRemaining().
hasRemaining() - Method in class VoxelBuffer: Are there voxels remaining in a buffer?
hasRemaining() - Method in class VoxelBufferUnsigned
hasSingleFeature() - Method in class SequentialSession
hasTemporary() - Method in class EncodedVoxels
HasTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A simple scheme for counting the touching voxels.
HasTouchingVoxels() - Constructor for class HasTouchingVoxels
hasVeryQuickPerInputExecution() - Method in class JobProcessor: Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class Task: Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class HelloWorld
hasVeryQuickPerInputExecution() - Method in class AggregateAnnotations
hasVeryQuickPerInputExecution() - Method in class CompareAnnotations
hasVeryQuickPerInputExecution() - Method in class ExportFeatures
hasVeryQuickPerInputExecution() - Method in class ConvertImageFormat
hasVeryQuickPerInputExecution() - Method in class GroupedStackBase
hasVeryQuickPerInputExecution() - Method in class ImageAssignLabel
hasVeryQuickPerInputExecution() - Method in class ScaleImage
hasVeryQuickPerInputExecution() - Method in class SegmentInstanceWithModel
hasVeryQuickPerInputExecution() - Method in class ExtractSlice
hasVeryQuickPerInputExecution() - Method in class MovieFromSlices
hasVeryQuickPerInputExecution() - Method in class CombineCSV
hasVeryQuickPerInputExecution() - Method in class CopyFiles
hasVeryQuickPerInputExecution() - Method in class SummarizeBase
hasVeryQuickPerInputExecution() - Method in class ConvertNamedChannels
hasVeryQuickPerInputExecution() - Method in class Develop
hasVeryQuickPerInputExecution() - Method in class ExportReportFeatures
hasVeryQuickPerInputExecution() - Method in class ExportObjectsAsCroppedImages
hasVeryQuickPerInputExecution() - Method in class ExportObjectsFromCSV
hasVeryQuickPerInputExecution() - Method in class SegmentMarksFromImage
hasWarningOccurred() - Method in interface ErrorReporter: Checks if at least one warning has been outputted.
hasWarningOccurred() - Method in class ErrorReporterBase
hasWarningOccurred() - Method in class ErrorReporterForTask
hasWrittenHeaders() - Method in class CSVWriter
HDF5ObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.hdf5: Writes a ObjectCollection to a HDF5 file.
HDF5ObjectsGenerator() - Constructor for class HDF5ObjectsGenerator: Creates with an element (and compressed set to true)
HDF5ObjectsGenerator(boolean) - Constructor for class HDF5ObjectsGenerator
HDF5PathHelper - Class in org.anchoranalysis.image.io.object: Paths to identify objects in the HDF5 for object-masks
head() - Method in class ContiguousVoxelPath
HeaderFormat - Class in org.anchoranalysis.plugin.io.bean.metadata.header: Populates ImageMetadata from the header of an image-file.
HeaderFormat() - Constructor for class HeaderFormat
headerNames(Optional<String>) - Method in class ExportReportFeatures
headers() - Method in class ReadByLine: The headers of the CSV file
headers(boolean) - Method in class FeatureSource: Generate label-headers for the non-feature-result columns in the CSV.
headers(boolean) - Method in class SingleRowPerInput
headers(boolean) - Method in class FromObjects
HelloWorld<S extends InputFromManager> - Class in org.anchoranalysis.launcher.run.tasks: A dummy task that simply writes a message to all log files, specifically: 1.
HelloWorld() - Constructor for class HelloWorld
help() - Method in class LauncherConfig: Config for displaying help message
HelpConfig - Class in org.anchoranalysis.launcher.config
HelpConfig(String, String) - Constructor for class HelpConfig
hexString() - Method in class RGBColor: Converts the red-blue-green values as a hex-string.
higherCountExistsThan(int) - Method in class PredicateAtCorner
higherCountExistsThan(int) - Method in class PredicateImplementation
higherCountExistsThan(int) - Method in interface VoxelsPredicate: Whether the count is greater than a particular threshold.
histogram() - Method in interface VoxelStatistics: A Histogram of all voxel values.
histogram() - Method in class VoxelStatisticsCombined
histogram() - Method in class VoxelStatisticsFromHistogram
Histogram - Class in org.anchoranalysis.math.histogram: A histogram of integer values.
Histogram(int) - Constructor for class Histogram: Constructs with a maximum value, and assuming a minimum value of 0.
Histogram(int, int) - Constructor for class Histogram: Constructs with a maximum value, and assuming a minimum value of 0.
histogram() - Method in class MultiInput
histogram(String) - Static method in class ReferenceFactory
Histogram.BinConsumer - Interface in org.anchoranalysis.math.histogram: Consumes a bin and corresponding count.
HistogramCSVGenerator - Class in org.anchoranalysis.image.io.histogram.output: Writes a histogram to a CSV file.
HistogramCSVGenerator() - Constructor for class HistogramCSVGenerator
HistogramCSVReader - Class in org.anchoranalysis.image.io.histogram.input
HistogramFactory - Class in org.anchoranalysis.image.voxel.statistics: Creates a Histogram to describe the intensity values of voxels in aggregate.
HistogramFixture - Class in org.anchoranalysis.test.feature.plugins
HistogramFromObjectsFactory - Class in org.anchoranalysis.image.core.object: Create a Histogram of the voxel intensity values in an image, pertaining to a region defined by a ObjectMask or a Mask.
HistogramProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Histogram.
HistogramProvider() - Constructor for class HistogramProvider
HistogramProviderUnary - Class in org.anchoranalysis.image.bean.provider
HistogramProviderUnary() - Constructor for class HistogramProviderUnary
histograms() - Method in class ImageInitialization
HISTOGRAMS - Static variable in class OutputterDirectories: Where collections of histograms are typically placed in a define-experiment output
HistogramStatistics - Class in org.anchoranalysis.math.histogram: Further statistics that can be derived from a histogram in addition to those existing as direct methods of Histogram.
HistogramThresholder - Class in org.anchoranalysis.plugin.image.intensity
HOGDescriptor - Class in org.anchoranalysis.plugin.opencv.bean.feature: Creates the entire HOG descriptor for an image.
HOGDescriptor() - Constructor for class HOGDescriptor
HOGFeature - Class in org.anchoranalysis.plugin.opencv.bean.feature: One part of a Histogram of Oriented Gradients descriptor, as applied to an image stack.
HOGFeature(SizeXY, int) - Constructor for class HOGFeature: Create with a specific size to resize to, and index.
HOGFeature() - Constructor for class HOGFeature
HOGParameters - Class in org.anchoranalysis.plugin.opencv.bean.feature: Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
HOGParameters() - Constructor for class HOGParameters
HomeSubdirectory - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
HomeSubdirectory() - Constructor for class HomeSubdirectory
HorizontalCacheCreator - Class in org.anchoranalysis.feature.session.cache
HorizontalCacheCreator(FeatureList<? extends FeatureInput>, SharedFeatures, FeatureInitialization, Logger) - Constructor for class HorizontalCacheCreator
HSB - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a sequence of colors by varying the hue-component in a HSB color model.
HSB() - Constructor for class HSB
HungarianAlgorithm - Class in org.anchoranalysis.math.optimization: An implementation of the Hungarian algorithm for solving the assignment problem.
HungarianAlgorithm(double[][]) - Constructor for class HungarianAlgorithm: Construct an instance of the algorithm.

I

idAndIncrement() - Method in class MarkWithIdentifierFactory
Identifiable - Interface in org.anchoranalysis.overlay.identifier
IdentifiablePair<T extends Identifiable> - Class in org.anchoranalysis.mpp.pair: Pair of marks
IdentifiablePair(T, T) - Constructor for class IdentifiablePair
identifier(Optional<String>) - Method in class ExperimentIdentifier: Creates an identifier for the experiment
identifier(Optional<String>) - Method in class ExperimentIdentifierAuto
identifier(Optional<String>) - Method in class ExperimentIdentifierConstant
identifier() - Method in class SingleFileInputBase
identifier() - Method in interface InputFromManager: A unique name associated with the input.
identifier() - Method in class InputFromManagerDelegate
identifier() - Method in class MultiInput
identifier() - Method in class Mark
identifier() - Method in class CoupledManifests
identifier() - Method in class ManifestCouplingDefinition
identifierAsPath() - Method in interface InputFromManager: Like InputFromManager.identifier() but converts the identifier to a path.
IdentifierFromMark - Class in org.anchoranalysis.mpp.mark
IdentifierFromMark() - Constructor for class IdentifierFromMark
IdentifierFromOverlay - Class in org.anchoranalysis.overlay.identifier
IdentifierFromOverlay() - Constructor for class IdentifierFromOverlay
IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter: Gets a unique identifier for a particular element at a particular iteration point.
IdentifyDelegateToOverlays - Class in org.anchoranalysis.overlay.identifier
IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection) - Constructor for class IdentifyDelegateToOverlays
IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection, boolean) - Constructor for class IdentifyDelegateToOverlays
IdentifyFromIteration<T> - Class in org.anchoranalysis.core.identifier.getter: Identify an element uniquely only by its iteration timepoint.
IdentifyFromIteration() - Constructor for class IdentifyFromIteration
IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a unique id number to each object.
IdentifyObjects() - Constructor for class IdentifyObjects
Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
Identity() - Constructor for class Identity
IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
IdentityImposeValueRelationToHistogram() - Constructor for class IdentityImposeValueRelationToHistogram
idFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes: ID for a particular object
IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional: The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case)
IfCondition() - Constructor for class IfCondition
IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Calculates a value if a condition lies within a certain range, otherwise returns constants
IfConditionWithinRange() - Constructor for class IfConditionWithinRange
IfElse - Class in org.anchoranalysis.image.io.bean.object.draw: Branches to two different writers depending on a binary condition.
IfElse(IfElse.Condition, DrawObject, DrawObject) - Constructor for class IfElse
IfElse() - Constructor for class IfElse
IfElse.Condition - Interface in org.anchoranalysis.image.io.bean.object.draw
IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.
IfGreaterThan() - Constructor for class IfGreaterThan
IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
IfHighLow() - Constructor for class IfHighLow
IfIncrementingNumberRequested - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Multiplexes between two PathPrefixers depending on whether an incrementing number sequence was output was requested.
IfIncrementingNumberRequested() - Constructor for class IfIncrementingNumberRequested
IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
IfKeyValueCondition() - Constructor for class IfKeyValueCondition
IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.
IfLessThan() - Constructor for class IfLessThan
IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if it's non-empty (at least one on voxel) otherwise maskElse is returned.
IfNotEmpty() - Constructor for class IfNotEmpty
IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
IfObjectFilter() - Constructor for class IfObjectFilter
ifOptionWithoutArgument(String, Consumer<T>) - Method in class AddOptionsFromCommandLine: Executes consumer if an option exists without any argument.
ifOptionWithSingleArgument(String, CheckedBiConsumer<T, String, E>) - Method in class AddOptionsFromCommandLine: Executes consumer if an option exists with a single argument.
IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Clamps a value if it lies outside the range - instead returning particular constants if below or above an acceptable range
IfOutsideRange() - Constructor for class IfOutsideRange
IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider: Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
IfParamEqual() - Constructor for class IfParamEqual
IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
IfParamEquals() - Constructor for class IfParamEquals
IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Base class which multiplexes between the current mask and an alternative depending if a condition is met.
IfPredicateBase() - Constructor for class IfPredicateBase
ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class OptionalUtilities: Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class CommandLineExtracter: Executes a Consumer if an option is present.
ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class AddOptionsFromCommandLine
IfRelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer: Multiplexes between two namers depending on if the relative-to-directory option is selected.
IfRelativeToDirectory() - Constructor for class IfRelativeToDirectory
IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is a particular stack exists (at least one on voxel) otherwise maskElse is returned.
IfStackExists() - Constructor for class IfStackExists
IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Creates a new channel which is a merged version of two input channels according to rules.
IfVoxelZero() - Constructor for class IfVoxelZero
IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed unless the name's first character is an underscore.
IgnoreUnderscorePrefix() - Constructor for class IgnoreUnderscorePrefix
IgnoreUnderscorePrefixUnless - Class in org.anchoranalysis.io.output.bean.rules: Like IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs are explicitly specified.
IgnoreUnderscorePrefixUnless(StringSet) - Constructor for class IgnoreUnderscorePrefixUnless: Create with first-level output names
IgnoreUnderscorePrefixUnless() - Constructor for class IgnoreUnderscorePrefixUnless
image() - Method in class MarksInitialization
ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Assigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.
ImageAssignLabel() - Constructor for class ImageAssignLabel
ImageBean<T> - Class in org.anchoranalysis.image.bean: A bean that must be initialized with ImageInitialization before usage.
ImageBean() - Constructor for class ImageBean
ImageCounter<T> - Interface in org.anchoranalysis.plugin.annotation.counter: Counts images on aggregate, some with associated annotations, others without.
ImageCounterList<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.counter: Allows operations to be applied to several ImageCounters collectively.
ImageCounterList() - Constructor for class ImageCounterList
ImageCounterWithStatistics<T> - Interface in org.anchoranalysis.plugin.annotation.counter: Like ImageCounter but also exports statistics.
ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
ImageCSVLabeller() - Constructor for class ImageCSVLabeller
ImageCSVLabellerInitialization - Class in org.anchoranalysis.plugin.image.task.labeller
ImageCSVLabellerInitialization(FileLabelMap<String>) - Constructor for class ImageCSVLabellerInitialization
ImageFileAttributes - Class in org.anchoranalysis.image.core.stack: Timestamps and other metadata associated with an image file-path, but not with the file's contents.
ImageFileAttributes(Path, ZonedDateTime, ZonedDateTime) - Constructor for class ImageFileAttributes
ImageFileEncoding - Class in org.anchoranalysis.io.bioformats.copyconvert: How values are encoded into an image-file.
ImageFileEncoding(boolean, boolean, int) - Constructor for class ImageFileEncoding
ImageFileFormat - Enum in org.anchoranalysis.core.format: A type of image format that are read/written to the filesystem, together with the extensions it may use.
ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert: How to shape the image (across various dimensions) after the copying
ImageFileShape(Dimensions, int, int) - Constructor for class ImageFileShape
ImageInitialization - Class in org.anchoranalysis.image.bean.nonbean.init
ImageInitialization(SharedObjects) - Constructor for class ImageInitialization
ImageInitialization(SharedObjects, Optional<ImageSizeSuggestion>) - Constructor for class ImageInitialization
ImageInitializationFactory - Class in org.anchoranalysis.image.io
ImageIOException - Exception in org.anchoranalysis.image.io
ImageIOException(String) - Constructor for exception ImageIOException
ImageIOException(String, Throwable) - Constructor for exception ImageIOException
ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
ImageIOWriter() - Constructor for class ImageIOWriter
ImageJConversionException - Exception in org.anchoranalysis.io.imagej.convert: When conversion to ImageJ data/type is not possible, or an error occurs during conversion.
ImageJConversionException(String) - Constructor for exception ImageJConversionException: Creates with a message.
ImageJConversionException(Exception) - Constructor for exception ImageJConversionException: Creates with a message.
ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Base class for writing a raster using ImageJ.
ImageJRasterWriter() - Constructor for class ImageJRasterWriter
ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image: A single label that is associated with an image.
ImageLabelAnnotation(String) - Constructor for class ImageLabelAnnotation
ImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image: Reads an ImageLabelAnnotation from the file-system.
ImageLabelAnnotationReader() - Constructor for class ImageLabelAnnotationReader
ImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image: Writes an ImageLabelAnnotation to the file-system.
ImageLabelAnnotationWriter() - Constructor for class ImageLabelAnnotationWriter
ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Associates a label with an image.
ImageLabeller() - Constructor for class ImageLabeller
ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Maps one set of labels to another
ImageLabellerStringMap() - Constructor for class ImageLabellerStringMap
ImageLabellerStringMapInitialization<T> - Class in org.anchoranalysis.plugin.image.task.labeller
ImageLabellerStringMapInitialization(Map<String, String>, T) - Constructor for class ImageLabellerStringMapInitialization
ImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Assigns a single label per image, as a whole.
ImageLabelStrategy() - Constructor for class ImageLabelStrategy
ImageMetadata - Class in org.anchoranalysis.image.core.stack: Information about an image, but not about the intensity or content of image voxels.
ImageMetadata(Dimensions, int, int, boolean, int, ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class ImageMetadata
ImageMetadataInput - Class in org.anchoranalysis.image.io.stack.input: An input that provides a ImageMetadata but only lazily when first called.
ImageMetadataInput(NamedFile, CheckedSupplier<ImageMetadata, ImageIOException>) - Constructor for class ImageMetadataInput: Create for a particular file and metadata.
ImageMetadataReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader: Reads an ImageMetadata from the file-system.
ImageMetadataReader() - Constructor for class ImageMetadataReader
ImageMoments - Class in org.anchoranalysis.math.statistics.moment: The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of points.
ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class ImageMoments: Calculates the second-moments from the covariance of a matrix of points.
ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: A base class for features that are calculated using image-moments.
ImageMomentsBase() - Constructor for class ImageMomentsBase
ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarizes the size of images.
ImageSize() - Constructor for class ImageSize
ImageSizeSuggestion - Interface in org.anchoranalysis.image.core.dimensions.size.suggestion: A suggestion on a size for an image.
ImageSizeSuggestionFactory - Class in org.anchoranalysis.image.core.dimensions.size.suggestion: Creates a ImageSizeSuggestion.
ImageTimestampsAttributes - Class in org.anchoranalysis.image.io.stack.input: This combines ImageFileAttributes plus a timestamp for image-acqusition.
ImageTimestampsAttributes(ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class ImageTimestampsAttributes
ImageTimestampsAttributesFactory - Class in org.anchoranalysis.io.bioformats.metadata: Derives ImageTimestampsAttributes from a file, additionally checking for EXIF metadata.
ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
ImgLib2Lanczos() - Constructor for class ImgLib2Lanczos
ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
ImgLib2Linear() - Constructor for class ImgLib2Linear
immutableAdd(Point2i, Point2i) - Static method in class Point2i: Adds two points immutably.
immutableAdd(Tuple3d, Tuple3d) - Static method in class Point3d: Adds two tuples immutably.
immutableAdd(Point3d, int, int, int) - Static method in class Point3d: Adds values to a point immutably.
immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i: Adds two tuples immutably.
immutableAdd(ReadableTuple3i, int, int, int) - Static method in class Point3i: Adds values to a tuple immutably.
immutableScale(Tuple3d, int) - Static method in class Point3d: Scales a tuple immutably.
immutableScale(ReadableTuple3i, int) - Static method in class Point3i: Multiplies each component by factor without changing any values in an existing point.
immutableSubtract(Tuple3d, Tuple3d) - Static method in class Point3d: Subtracts a Tuple3d from a Tuple3d immutably.
immutableSubtract(Tuple3i, Tuple3d) - Static method in class Point3d: Subtracts a Tuple3d from a Tuple3i immutably.
immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i: Subtracts two tuples immutably.
ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Imposes minima in seed locations on the input-channel before performing the segmentation
ImposeMinima() - Constructor for class ImposeMinima
imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class MinimaImposition
imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class MinimaImpositionGrayscaleReconstruction
imposeMinimumRadius(double) - Method in class FitResult
ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Adds an explicit Resolution to an image after it has been read.
ImposeResolution() - Constructor for class ImposeResolution
IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory: Defines an AnchorBean in a separate file on the file-system.
IncludeBeanFactory() - Constructor for class IncludeBeanFactory
includeFirst() - Method in class MergedPairsInclude
includeFirstOrSecond() - Method in class MergedPairsInclude
includeGroupInExperiment(boolean) - Method in class FeatureSource: Iff true, group columns are added to the CSV exports, and other group exports may occur in sub-directories.
includeGroupInExperiment(boolean) - Method in class FromHistogram
includeGroupInExperiment(boolean) - Method in class FromImage
includeGroupInExperiment(boolean) - Method in class FromImageMetadata
includeGroupInExperiment(boolean) - Method in class FromObjects: If either a group-generator is defined or there's more than one provider, then groups should be included.
IncludeListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory: Like ListBeanFactory but also includes elements in other lists defined in the include tag.
IncludeListBeanFactory() - Constructor for class IncludeListBeanFactory: Default constructor.
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaOr
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class ArbitraryPointCommon
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class BoundingBoxIntersection
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaFeatureRelationThreshold
IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
IncludeMarksFailureException(String) - Constructor for exception IncludeMarksFailureException
IncludeMarksFailureException(Exception) - Constructor for exception IncludeMarksFailureException
includeMerged() - Method in class MergedPairsInclude
IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points: 1.
IncludeRandomObjects() - Constructor for class IncludeRandomObjects
includeSecond() - Method in class MergedPairsInclude
IncompleteElementRange - Interface in org.anchoranalysis.io.manifest.sequencetype: An incomplete range of discrete integers (like IndexRangeSeek but with a string-representation for each index.
IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions: When an image has incompatible image-size with expectations.
IncorrectImageSizeException(String) - Constructor for exception IncorrectImageSizeException: Create with a message.
IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype: When an unexpected VoxelDataType is encountered.
IncorrectVoxelTypeException(String) - Constructor for exception IncorrectVoxelTypeException: Create with only a message.
IncorrectVoxelTypeException(Throwable) - Constructor for exception IncorrectVoxelTypeException: Create with only a cause.
incr(int) - Method in class AggIDCounter
incr(Reporting<S>) - Method in class PeriodTriggerBank
IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class IncreaseFeatureCondition
increasingIntegers(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
IncreasingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype: Indices must be integers that always increase as added.
IncreasingIntegers() - Constructor for class IncreasingIntegers
increment() - Method in class Counter: Increases the counter by one.
increment(double) - Method in class RunningSum: Adds a new item to the sum, and increments the count by 1.
increment(double, long) - Method in class RunningSum: Increments both the sum and count by particular values.
increment(RunningSum) - Method in class RunningSum: Increments (adds) an existing RunningSum to the current.
increment(Point2i) - Method in class RunningSumPoint: Increments the running-sum by a Point2i.
increment(Point2d) - Method in class RunningSumPoint: Increments the running-sum by a Point2d.
increment(Point3i) - Method in class RunningSumPoint: Increments the running-sum by a Point3i.
increment(Point3d) - Method in class RunningSumPoint: Increments the running-sum by a Point3d.
increment(Tuple3d) - Method in class Tuple3d: Increments each component's value by the corresponding value in a Tuple3d.
incrementBy(int) - Method in class Counter: Increases the counter by a specific value.
incrementChild() - Method in class ProgressMultiple: Increments the current child tracker to the next child.
incrementCount(T) - Method in class SummarizerImageMetadata
incrementCount(T) - Method in class FrequencyMap
incrementCounter() - Method in class RecordingCounter: Increments the counter.
incrementEnergy(double) - Method in class Aggregator
incrementIndexOnly() - Method in class KernelPointCursor: Increments the current index state by one, without changing the current point state.
incrementingByOne(String, OutputterChecked) - Method in class OutputSequenceStackFactory: Creates an sequence of stacks in a subdirectory with a number in the outputted file name that increments each time by one.
incrementingByOne(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory: Writes elements to directory, with an incrementing integer in the filename.
incrementingByOneCurrentDirectory(String, String, int, OutputterChecked) - Method in class OutputSequenceStackFactory: Creates a sequence of stacks in the current context's directory with a number in the outputted file name that increments each time by one.
incrementingByOneCurrentDirectory(String, String, int) - Method in class OutputSequenceFactory: Writes elements to the current directory, with an incrementing integer in the filename.
incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class OutputSequenceFactory: Writes file for each element in a stream with an incrementing integer sequence in the outputted file-name.
incrementingIntegers(OutputPatternIntegerSuffix, int, int) - Method in class OutputSequenceFactory
IncrementingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
IncrementingIntegers() - Constructor for class IncrementingIntegers
IncrementingIntegers(int) - Constructor for class IncrementingIntegers
IncrementingIntegers(int, int) - Constructor for class IncrementingIntegers
IncrementingNumber - Class in org.anchoranalysis.io.output.bean.path.prefixer: Outputs an incrementing number for each output that occurs.
IncrementingNumber(String) - Constructor for class IncrementingNumber
IncrementingNumber() - Constructor for class IncrementingNumber
incrementKernelAcceptance(int) - Method in class Aggregator
incrementKernelProp(int) - Method in class Aggregator
incrementSize(double) - Method in class Aggregator
incrementTemperature(double) - Method in class Aggregator
incrementValue(int) - Method in class Histogram: Increments the count for a particular value by one.
incrementValueBy(int, int) - Method in class Histogram: Increments the count for a particular value.
incrementValueBy(int, long) - Method in class Histogram: Like Histogram.incrementValueBy(int, int) but accepts a long as the increase argument.
incrementX() - Method in class KernelPointCursor: Increments the point and associated index by one in the X dimension.
incrementX() - Method in class Point2i: Increments the X component's value by one.
incrementX(int) - Method in class Point2i: Increments the X component's value by a shift.
incrementX(double) - Method in class Tuple3d: Increments the X component's value by a shift.
incrementX() - Method in class Tuple3i: Increments the X component's value by one.
incrementX(int) - Method in class Tuple3i: Increments the X component's value by a shift.
incrementXTwice() - Method in class KernelPointCursor: Increments the point and associated index by two in the X dimension.
incrementY() - Method in class KernelPointCursor: Increments the point and associated index by one in the Y dimension.
incrementY() - Method in class Point2i: Increments the Y component's value by one.
incrementY(int) - Method in class Point2i: Increments the Y component's value by a shift.
incrementY(double) - Method in class Tuple3d: Increments the Y component's value by a shift.
incrementY() - Method in class Tuple3i: Increments the Y component's value by one.
incrementY(int) - Method in class Tuple3i: Increments the Y component's value by a shift.
incrementYTwice() - Method in class KernelPointCursor: Increments the point and associated index by two in the Y dimension.
incrementZ() - Method in class KernelPointCursor: Increments the point by one in the Z dimension.
incrementZ(double) - Method in class Tuple3d: Increments the Z component's value by a shift.
incrementZ() - Method in class Tuple3i: Increments the Z component's value by one.
incrementZ(int) - Method in class Tuple3i: Increments the Z component's value by a shift.
incrementZTwice() - Method in class KernelPointCursor: Increments the point by two in the Z dimension.
IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts each channel independently and creates a single-channeled stack from the conversion.
IndependentChannels() - Constructor for class IndependentChannels
index(int, int, Extent) - Method in enum OrientationChange: Determines the index in a output-array to put an element after applying the orientation-change.
index(int, int, int, Extent) - Method in enum OrientationChange: Like {#link determineOutputIndex(int,int,Extent)} but also accepts an index.
index(int) - Method in class IntegerRange: Maps an original integer to it's index from (0..size]
Indexable - Class in org.anchoranalysis.core.index: Holds a single-index which is hashable and comparable.
Indexable(int) - Constructor for class Indexable
IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class IndexableMarksWithEnergy
IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: An output-name with an index somehow appended or prepended in a particular style.
IndexableOutputNameStyle() - Constructor for class IndexableOutputNameStyle
IndexableOutputNameStyle(String) - Constructor for class IndexableOutputNameStyle
IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class IndexableOutputNameStyle: Copy constructor
IndexableOverlays - Class in org.anchoranalysis.overlay
IndexableOverlays(int, OverlayCollection) - Constructor for class IndexableOverlays
IndexByChannel<T> - Class in org.anchoranalysis.mpp.index
IndexByChannel() - Constructor for class IndexByChannel
IndexByRegion<T> - Class in org.anchoranalysis.mpp.index
IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class IndexByRegion
indexDistanceMaxToClosestPoint(Point3i, List<ContiguousVoxelPath>, int) - Static method in class FindMinimumDistance: The index of whichever of the ContiguousPixelPaths has the nearest point
IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv: Stores the rows from the CSV file.
IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class IndexedCSVRows: Creates an index of the rows of the CSV file according to a particular columnDefinition
IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region: MarkRegion with a region and an index
IndexedRegionBase() - Constructor for class IndexedRegionBase
indexIncr(String) - Method in class SequenceMemory
indexInitialPoint() - Method in class ContiguousVoxelPath
indexOf(String) - Method in class FeatureNameMapToIndex: The index for a particular featureName
indexOf(Mark) - Method in class VoxelizedMarksWithEnergy
indexOf(Object) - Method in class UpdatableMarksList
indexOf(Mark) - Method in class MarkCollection
IndexRange - Interface in org.anchoranalysis.core.index.range: A range of discrete integers with a minimum and a maximum.
IndexRangeNegative - Class in org.anchoranalysis.core.index.range: Specifying a sub-range of indices, tolerating also negative indices.
IndexRangeNegative(int, int) - Constructor for class IndexRangeNegative
IndexRangeNegativeFactory - Class in org.anchoranalysis.core.index.range: Creates IndexRangeNegative.
IndexRangeSeek - Interface in org.anchoranalysis.core.index.range: A range of discrete integers, where one can always find the succeeding or preceding index.
indexUniquePixel - Variable in class ColumnDefinition
InferFromHeader - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: Tries to construct the ImageMetadata from EXIF and other metadata, if available, or otherwise falls back to another reader.
InferFromHeader() - Constructor for class InferFromHeader
InferFromHeader(ImageMetadataReader, List<HeaderFormat>) - Constructor for class InferFromHeader
informLatestState(T) - Method in class Kernel: Called every time a proposal is accepted, so a kernel can potentially keep track of the state of the current image
informLatestState(T) - Method in class KernelIndependent
initBeforeCalc(KernelCalculationContext) - Method in class Kernel
initBeforeCalc(KernelCalculationContext) - Method in class KernelIndependent
initBeforeCalc(KernelCalculationContext) - Method in class KernelProposer
initHeaders(String[]) - Method in class ColumnDefinition
initHeaders(String[]) - Method in class Pairwise
initHeaders(String[]) - Method in class Single
InitializableBean<B,P extends BeanInitialization> - Class in org.anchoranalysis.bean.initializable: A bean that must be initialized with some parameters before being used.
InitializableBean(BeanInitializer, InitializationParameterAssigner) - Constructor for class InitializableBean
InitializationContext - Class in org.anchoranalysis.experiment.io: Context for creating initialization-parameters.
InitializationContext(InputOutputContext) - Constructor for class InitializationContext
InitializationContext(InputOutputContext, Optional<ImageSizeSuggestion>) - Constructor for class InitializationContext
InitializationFactory - Class in org.anchoranalysis.image.feature.calculator
InitializationFactory - Class in org.anchoranalysis.plugin.image.task.stack
InitializationParameterAssigner - Interface in org.anchoranalysis.bean.initializable.property: Assigns a parameter to a bean, if the bean accepts it.
InitializationWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
InitializationWithEnergyStack(EnergyStack, InitializationContext) - Constructor for class InitializationWithEnergyStack
InitializationWithEnergyStack(ImageInitialization, EnergyStack) - Constructor for class InitializationWithEnergyStack
initialize(P, Logger) - Method in class InitializableBean: Initializes the bean with the necessary parameters.
initialize(FeatureInitialization, Logger) - Method in interface FeatureCalculationCache: Initializes the cache.
initialize(ArrangeStack, List<RGBStack>) - Method in class RasterArranger
initialize(List<Histogram>, Optional<Dictionary>) - Method in class VoxelScore: Initializes the voxels-score.
initialize(ChannelGetter, InputOutputContext) - Method in class ChannelFilter
initialize(Path) - Method in class Manifest
initialize(BeanInstanceMap) - Method in class OutputWriteSettings
initialize() - Method in class MarksWithEnergyBreakdown
initialize(VoxelPartitionFactory<T>, int, int, int) - Method in class IndexByChannel
initialize(MarksInitialization, Logger) - Method in class ReportFeatureEvaluator
initialize(Generator<T>) - Method in class PeriodicSubdirectoryReporter
initialize() - Method in class KernelProposer
initialize() - Method in class TerminationCondition: Called before TerminationCondition.continueFurther(int, double, int, org.anchoranalysis.core.log.MessageLogger) once to setup state in the bean.
initialize() - Method in class TerminationConditionListOr
initialize() - Method in class TriggerTerminationCondition
initialize(List<Histogram>, Optional<Dictionary>) - Method in class CalculateLevelBase
initialize(List<Histogram>, Optional<Dictionary>) - Method in class FromDictionaryBase
initialize(List<Histogram>, Optional<Dictionary>) - Method in class IdentityImposeValueRelationToHistogram
initialize(List<Histogram>, Optional<Dictionary>) - Method in class NormalizeByMax
initialize(Logger) - Method in interface AfterCondition
initialize(Logger) - Method in class IncreaseFeatureCondition
initialize(Path) - Method in class BinaryOutcomeImageLabeller
initialize(Path) - Method in class ImageCSVLabeller
initialize(Path) - Method in class ImageLabeller: Should be called once before calling any other methods
initialize(Path) - Method in class ImageLabellerStringMap
initialize(KernelBirth<T>, KernelDeath<T>) - Method in class KernelReplace: Must be called before makeProposal
initialize() - Method in class NumberIterations
initialize() - Method in class UnchangedBase
initialize() - Method in class UnchangedScore
initialize() - Method in class UnchangedSize
InitializeException - Exception in org.anchoranalysis.core.exception: An exception that occurs when initializing something, and it doesn't succeed
InitializeException(String) - Constructor for exception InitializeException: Creates with a message, but without a cause.
InitializeException(Throwable) - Constructor for exception InitializeException: Creates with a cause, but without a message.
InitializeException(String, Throwable) - Constructor for exception InitializeException: Creates with message and cause.
initializePhase(int) - Method in class HungarianAlgorithm: Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
initializeRecursive(P, Logger) - Method in class InitializableBean: Initializes this object, and all children objects, so long as they have P once a Bean doesn't have P, the children are not evaluated.
initializeRecursive(Logger) - Method in class NullParametersBean: Initialize this bean and any suitable child beans.
initializeRecursive(FeatureInitialization, Logger) - Method in class FeatureList: Initializes all features in the list, and recursively any features they contain.
initializeRecursive(FeatureInitialization, Logger) - Method in class SharedFeaturesSubset: Initialize all features in this instance, recursively also initializating any child-features.
initializerForMarksBeans() - Static method in class MarksBean: Creates a property-initializes for MPP-Beans
initialKernel() - Method in class KernelProposer
initRecursiveWithInitializer(BeanInitializer<?>, Logger) - Method in class InitializableBean: Initializes the bean and recursively all contained beans (who have compatible initialization requirements)
initSource(int, int) - Method in interface ProcessChangedPointAbsoluteMasked: The value and offset for the source point (around which we process neighbors).
initSource(Point3i, int, int) - Method in interface ProcessVoxelNeighbor: Specify the source-point (of which all the processed points are neighbors).
initSource(int, int) - Method in interface ProcessVoxelNeighborAbsolute: The value and offset for the source point (around which we process neighbors).
initSource(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class RandomCollectionWithAddCriteria
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class EnergySavedPairs
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class UpdatableMarksList
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in interface UpdatableMarks
initWithProposerSharedObjects(MarksInitialization, Logger) - Method in class KernelProposer
input() - Method in class ExecutionArguments: Arguments to help determine the input to the experiment.
INPUT_IMAGE - Static variable in class StackIdentifiers: The image used as the primary input for a task.
InputArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's input in addition to its bean specification.
InputArguments() - Constructor for class InputArguments
InputBound<T,S> - Class in org.anchoranalysis.experiment.task: Input for executing a task, associated with shared-state and other parameters.
InputBound(T, S, Manifest, boolean, InputOutputContextStateful, InputOutputContextStateful) - Constructor for class InputBound
InputContextParameters - Class in org.anchoranalysis.io.input: Additional parameters that offer context for many beans that provide input-functions.
InputContextParameters() - Constructor for class InputContextParameters
InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for inputs.
InputFromManager - Interface in org.anchoranalysis.io.input: One particular input for processing.
InputFromManagerDelegate<T extends InputFromManager> - Class in org.anchoranalysis.io.input: A base class for InputFromManager-implementing classes that delegate to another.
InputFromManagerDelegate(T) - Constructor for class InputFromManagerDelegate
InputManager<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean: Base class for describing the inputs.
InputManager() - Constructor for class InputManager
InputManagerParameters - Class in org.anchoranalysis.io.input.bean: Parameters passed to an InputManager to generate input-objects
InputManagerParameters(Logger) - Constructor for class InputManagerParameters: Create with only a logger, and using sensible default values for the other fields.
InputManagerParameters(InputContextParameters, Progress, ExecutionTimeRecorder, Logger) - Constructor for class InputManagerParameters
InputManagerUnary<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean: Base class for an InputManager that delegates to another InputManager with the same input-type.
InputManagerUnary() - Constructor for class InputManagerUnary
InputManagerWithStackReader<T extends InputFromManager> - Class in org.anchoranalysis.image.io.bean.stack.reader
InputManagerWithStackReader() - Constructor for class InputManagerWithStackReader
inputName() - Method in class StackWithMap
inputName() - Method in class SegmentObjectsFromONNXModel
inputName() - Method in class SegmentObjectsFromTensorFlowModel
inputOutput(ExecutionArguments, OutputterChecked) - Method in class ExperimentFeedbackContext
InputOutputContext - Interface in org.anchoranalysis.io.output.outputter: A context for performing input generally and outputting to a particular output-directory.
InputOutputContextStateful - Class in org.anchoranalysis.experiment.task: This exists as an implementation of InputOutputContext that exposes a StatefulMessageLogger.
InputOutputContextStateful(ExecutionArguments, Outputter, ExecutionTimeRecorder, StatefulMessageLogger, ErrorReporter) - Constructor for class InputOutputContextStateful
InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter: Caches a InputOutputContext for each subdirectory as they are created.
InputOutputContextSubdirectoryCache(InputOutputContext, ManifestDirectoryDescription, boolean) - Constructor for class InputOutputContextSubdirectoryCache
InputOutputExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.io: An experiment that uses both an InputManager to specify inputs and a OutputManager to specify outputting.
InputOutputExperiment() - Constructor for class InputOutputExperiment
InputReadFailedException - Exception in org.anchoranalysis.io.input
InputReadFailedException(String) - Constructor for exception InputReadFailedException
InputReadFailedException(Throwable) - Constructor for exception InputReadFailedException
InputReadFailedException(String, Throwable) - Constructor for exception InputReadFailedException
inputs(InputManagerParameters) - Method in class AnnotationInputManager
inputs(InputManagerParameters) - Method in class InputManager: Creates a list of inputs given particular parameters.
inputs(InputManagerParameters) - Method in class InputManagerUnary
inputs() - Method in class InputsWithDirectory: The inputs.
inputs(InputManagerParameters) - Method in class MultiInputManager
inputs(InputManagerParameters) - Method in class AnnotationComparisonInputManager
inputs(InputManagerParameters) - Method in class GroupFiles
inputs(InputManagerParameters) - Method in class NamedChannels
inputs(InputManagerParameters) - Method in class NamedChannelsAppend
inputs(InputManagerParameters) - Method in class Concatenate
inputs(InputManagerParameters) - Method in class NamedFiles
inputs(InputManagerParameters) - Method in class NamedFilesWithDirectory
inputs(InputManagerParameters) - Method in class CoupledManifestsInputManager
inputs(InputManagerParameters) - Method in class ConvertNamedChannelsToStack
inputs(InputManagerParameters) - Method in class Stacks
inputs(ImageInitialization, Logger) - Method in class ExportObjectsBase
inputs(InputManagerParameters) - Method in class FromCSVInputManager
inputs(InputManagerParameters) - Method in class MultiInputManagerQuick
inputs(InputManagerParameters) - Method in class NamedChannelsQuick
inputSelectParam(CommandLine) - Static method in class SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an input manager a directory, set as an the inputDirectory in the input-context a string with a wild-card, assumed to be a glob, set into the input-context as a glob a string with a period and without any forward or backwards slashes, set into the input-context as an extension to match
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class InputManagerUnary: Calculates the inputs to return given the inputs from the delegate.
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class BranchIfDebug
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Exclude
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterCSVColumn
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterDescriptiveName
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterIfDebug
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Limit
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Shuffle
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class ShuffleIfRequested
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class SortAlphabetically
InputsWithDirectory<T extends InputFromManager> - Class in org.anchoranalysis.io.input: All inputs for an experiment, together with any parent directory which is specified as a parent for these inputs.
InputsWithDirectory(List<T>) - Constructor for class InputsWithDirectory: Creates without any parent directory.
InputsWithDirectory(List<T>, Optional<Path>) - Constructor for class InputsWithDirectory
inputType() - Method in class Feature: The class corresponding to feature input-type.
inputType() - Method in class FeatureBinary
inputType() - Method in class FeatureFromList
inputType() - Method in class FeatureGeneric
inputType() - Method in class FeatureUnary
inputType() - Method in class FeatureResults
inputType() - Method in class FeatureEnergy
inputType() - Method in class FeatureHistogram
inputType() - Method in class FeatureImageMetadata
inputType() - Method in class FeatureStack
inputType() - Method in class FeatureObjectCollection
inputType() - Method in class FeaturePairObjects
inputType() - Method in class FeatureSingleObject
inputType() - Method in class AsSingle
inputType() - Method in class FeatureAllMemo
inputType() - Method in class FeaturePairMemo
inputType() - Method in class FeatureSingleMemo
inputType() - Method in class FeatureMarkCollection
inputType() - Method in class FeatureMark
inputType() - Method in class FromDimensionsBase
inputType() - Method in class FeatureSingleObjectFromShared
inputType() - Method in class AsMark
inputType() - Method in class AsObject
inputTypesExpected() - Method in class Task: Highest class(es) that will function as a valid input.
InputTypesExpected - Class in org.anchoranalysis.experiment.task: A list of base (parent) classes for input-types that a task expects
InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class InputTypesExpected
inputTypesExpected() - Method in class HelloWorld
inputTypesExpected() - Method in class AggregateAnnotations
inputTypesExpected() - Method in class CompareAnnotations
inputTypesExpected() - Method in class ExportFeatures
inputTypesExpected() - Method in class FeatureSource: Highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class FromHistogram
inputTypesExpected() - Method in class FromImage
inputTypesExpected() - Method in class FromImageMetadata
inputTypesExpected() - Method in class GroupedStackBase
inputTypesExpected() - Method in class ImageAssignLabel
inputTypesExpected() - Method in class RasterTask
inputTypesExpected() - Method in class ScaleImage
inputTypesExpected() - Method in class SegmentInstanceWithModel
inputTypesExpected() - Method in class ExtractSlice
inputTypesExpected() - Method in class CombineCSV
inputTypesExpected() - Method in class CopyFiles
inputTypesExpected() - Method in class SummarizeInputs
inputTypesExpected() - Method in class ConvertNamedChannels
inputTypesExpected() - Method in class Develop
inputTypesExpected() - Method in class ExportReportFeaturesFromManifest
inputTypesExpected() - Method in class ExportReportFeaturesFromMulti
inputTypesExpected() - Method in class FromObjects
inputTypesExpected() - Method in class ExportObjectsAsCroppedImages
inputTypesExpected() - Method in class ExportObjectsFromCSV
inputTypesExpected() - Method in class SegmentMarksFromImage
insertAfter(List<Point3i>) - Method in class ContiguousVoxelPath: Inserts points at end of existing path.
insertBefore(List<Point3i>) - Method in class ContiguousVoxelPath: Inserts points before existing path.
insertBeginning(String) - Method in class FeatureNameList: Inserts a new feature-name at the beginning of the list.
insertBeginning(String[]) - Method in class FeatureNameList: Inserts new feature-names at the beginning of the list.
InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an out string where $digit$ is replaced with the #digit group from a regex
InsertRegExGroups() - Constructor for class InsertRegExGroups
InsertRegExGroups(RegEx, String) - Constructor for class InsertRegExGroups
instance() - Static method in class NullInitialization: Singleton instance of NullInitialization.
instance() - Static method in class ExecutionTimeRecorderIgnore: Singleton instance.
INSTANCE - Static variable in class NoSharedState
instance() - Static method in class FeatureInputNull: A singleton instance.
instance() - Static method in class DefaultChildCacheFinder
instance() - Static method in class ChannelFactory: Singleton instance of ChannelFactory.
INSTANCE - Static variable in class FloatVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class SignedShortVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class UnsignedByteVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class UnsignedIntVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class UnsignedShortVoxelType: A singleton instance of the type.
instance() - Static method in class VoxelsFactory: Singleton instance.
instance() - Static method in class ConfigureBioformatsLogging
INSTANCE - Static variable in class All: A singleton instance of All.
INSTANCE - Static variable in class IgnoreUnderscorePrefix: A singleton instance of IgnoreUnderscorePrefix.
INSTANCE - Static variable in class None: A singleton instance of None.
INSTANCE - Static variable in class Permissive: A singleton instance of Permissive.
instance() - Static method in class RegionMapSingleton
instance() - Static method in class ErrorNodeNull
instance() - Static method in class RootPathMap
InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
InsufficientPointsException() - Constructor for exception InsufficientPointsException
InsufficientPointsException(String, Throwable) - Constructor for exception InsufficientPointsException
InsufficientPointsException(String) - Constructor for exception InsufficientPointsException
InsufficientPointsException(Throwable) - Constructor for exception InsufficientPointsException
IntBinaryOperation - Interface in org.anchoranalysis.core.functional.unchecked: A binary operation on two int-values that produces an int.
IntegerList - Class in org.anchoranalysis.bean.primitive: A bean defining a list of Integers.
IntegerList(Integer...) - Constructor for class IntegerList: Constructs with one or more values added to the list.
IntegerListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a IntegerList from a XML element.
IntegerListFactory() - Constructor for class IntegerListFactory
IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
IntegerRange(int) - Constructor for class IntegerRange
IntegerRange(int, int) - Constructor for class IntegerRange
IntegerSet - Class in org.anchoranalysis.bean.primitive: A bean defining a set of Integers.
IntegerSet(Integer...) - Constructor for class IntegerSet: Constructs with one or more values added to the list.
IntegerSet() - Constructor for class IntegerSet
integerSet() - Method in class OverlayCollection
IntegerSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive: Creates a IntegerSet from a XML element.
IntegerSetFactory() - Constructor for class IntegerSetFactory
IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Outputs a file-name involving an integer of length numberDigits with leading zeros.
IntegerSuffixOutputNameStyle() - Constructor for class IntegerSuffixOutputNameStyle
IntegerSuffixOutputNameStyle(String, int) - Constructor for class IntegerSuffixOutputNameStyle
IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class IntegerSuffixOutputNameStyle
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Calculates a statistic from the intensity values covered by a single object-mask in a channel.
Intensity() - Constructor for class Intensity
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The intensity of a particular channel of the stack, by default the mean-intensity.
Intensity() - Constructor for class Intensity
Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
Intensity() - Constructor for class Intensity
IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
IntensityGradientBase() - Constructor for class IntensityGradientBase
IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
IntensityGreaterEqualThan() - Constructor for class IntensityGreaterEqualThan
intensityMax(Voxels<T>) - Static method in class IterateVoxelsAll: Finds the maximum intensity-value (as an int) among all voxels.
IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
IntensityMeanMaxSlice() - Constructor for class IntensityMeanMaxSlice
IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShell() - Constructor for class IntensityMeanShell
IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a shell around an object-mask using a standard dilation and erosion process
IntensityMeanShellBase() - Constructor for class IntensityMeanShellBase
IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShellMaxSlice() - Constructor for class IntensityMeanShellMaxSlice
IntensityMoments - Class in org.anchoranalysis.plugin.image.feature.bean.list: Calculate various moment-related statistics about the intensity of each channel of an image.
IntensityMoments() - Constructor for class IntensityMoments
interpolate(VoxelsUntyped, VoxelsUntyped) - Method in class Interpolator: Copies voxels slice-by-slice from source to destination performing necessary interpolation.
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class Interpolator: Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorNone
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorRecordExecutionTime
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorImageJ
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorOpenCV
interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class Interpolator: Interpolates from voxelsSource to voxelsDestination for float buffers.
interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorNone
interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorRecordExecutionTime
interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorImageJ
interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorOpenCV
InterpolateHelper - Class in org.anchoranalysis.image.voxel.interpolator: Helper utility functions for an Interpolator.
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class Interpolator: Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit buffers.
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorNone
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorRecordExecutionTime
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorImageJ
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorOpenCV
Interpolator - Class in org.anchoranalysis.image.voxel.interpolator: Copies voxels while performing interpolation.
Interpolator() - Constructor for class Interpolator
InterpolatorBean - Class in org.anchoranalysis.image.bean.interpolator
InterpolatorBean() - Constructor for class InterpolatorBean
InterpolatorBeanImageJ - Class in org.anchoranalysis.io.imagej.bean: Creates an Interpolator that uses ImageJ.
InterpolatorBeanImageJ() - Constructor for class InterpolatorBeanImageJ
InterpolatorBeanOpenCV - Class in org.anchoranalysis.plugin.opencv.bean.interpolate: Creates an Interpolator that uses OpenCV.
InterpolatorBeanOpenCV() - Constructor for class InterpolatorBeanOpenCV
InterpolatorFactory - Class in org.anchoranalysis.image.voxel.interpolator: Creates instances of Interpolator to match particular circumstances.
InterpolatorImageJ - Class in org.anchoranalysis.io.imagej.interpolator: An implementation of Interpolator that uses ImageJ.
InterpolatorImageJ() - Constructor for class InterpolatorImageJ
InterpolatorImgLib2 - Class in org.anchoranalysis.image.voxel.interpolator: Performs interpolation using ImgLib2.
InterpolatorImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Constructor for class InterpolatorImgLib2
InterpolatorImgLib2Lanczos - Class in org.anchoranalysis.image.voxel.interpolator: An interpolator that uses Lanczos resampling as implemented in Imglib2.
InterpolatorImgLib2Lanczos() - Constructor for class InterpolatorImgLib2Lanczos: Default constructor.
InterpolatorImgLib2Linear - Class in org.anchoranalysis.image.voxel.interpolator: An interpolator that uses linear interpolation as implemented in Imglib2.
InterpolatorImgLib2Linear() - Constructor for class InterpolatorImgLib2Linear: Default constructor.
InterpolatorImgLib2NearestNeighbor - Class in org.anchoranalysis.image.voxel.interpolator: An interpolator that uses nearest neighbor interpolation as implemented in Imglib2.
InterpolatorImgLib2NearestNeighbor() - Constructor for class InterpolatorImgLib2NearestNeighbor: Default constructor.
InterpolatorNone - Class in org.anchoranalysis.image.voxel.interpolator: Doesn't do any interpolation, just copies a single value for each voxel.
InterpolatorNone() - Constructor for class InterpolatorNone
InterpolatorOpenCV - Class in org.anchoranalysis.plugin.opencv.interpolator: Interpolates using OpenCV's cv2.resize function.
InterpolatorOpenCV() - Constructor for class InterpolatorOpenCV
InterpolatorRecordExecutionTime - Class in org.anchoranalysis.image.voxel.interpolator: Calls another Interpolator recording each interpolation call via a ExecutionTimeRecorder.
InterpolatorRecordExecutionTime(Interpolator, ExecutionTimeRecorder, String) - Constructor for class InterpolatorRecordExecutionTime: Creates with an Interpolator and ExecutionTimeRecorder.
intersect(ObjectMask, Extent) - Method in class ObjectMask: Intersects this object-mask with another
IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
IntersectingObjects<T> - Class in org.anchoranalysis.image.voxel.object: A data-structure to efficiently determine which object-masks intersect in a collection.
IntersectingObjects(Collection<T>, Function<T, ObjectMask>) - Constructor for class IntersectingObjects: Creates an r-tree for particular objects, as extracted from elements.
Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
Intersection() - Constructor for class Intersection
Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair: Finds the intersection of two objects and calculates a feature on it
Intersection() - Constructor for class Intersection
intersection() - Method in class BoundingBox: For evaluating the intersection between this bounding-box and others.
IntersectionOverUnion - Class in org.anchoranalysis.spatial.box: Calculates the intersection-over-union score for a pair of bounding-boxes.
intersectsWith(ObjectMask) - Method in class IntersectingObjects: All elements that intersect with a particular object.
intersectsWith(BoundingBox) - Method in class IntersectingObjects: All elements that intersect with a particular bounding box.
IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps objects which intersects with ANY ONE of a collection of other objects.
IntersectsWith() - Constructor for class IntersectsWith
intersectsWith(BoundingBox) - Method in class BoundingBoxRTree: Which bounding-boxes intersect with another specific bounding box?
intersectsWith(double, double) - Method in class IntervalRTree: Which bounding-boxes intersect with another specific bounding box?
IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Returns only the objects that intersect with at least one object in the container
IntersectsWithContainer() - Constructor for class IntersectsWithContainer
intersectsWithStream(ObjectMask) - Method in class IntersectingObjects: Like IntersectingObjects.intersectsWith(ObjectMask) but returns the objects as a Stream rather than a Set.
intersectsWithStream(BoundingBox) - Method in class BoundingBoxRTree: Like BoundingBoxRTree.intersectsWith(BoundingBox) but returns a Stream instead of a Set.
intersectsWithStream(double, double) - Method in class IntervalRTree: Like IntervalRTree.intersectsWith(double, double) but returns a Stream instead of a Set.
intersectsWithStream(Rectangle) - Method in class RTree: A stream of the elements that a rectangle intersects with.
intersectWith(Extent) - Method in class Extent: Intersects this extent with another (i.e.
IntervalRTree<T> - Class in org.anchoranalysis.spatial.rtree: An R-Tree that contains items, each with an associated one-dimensional interval.
IntervalRTree() - Constructor for class IntervalRTree: Creates an empty R-Tree.
IntervalRTree(int) - Constructor for class IntervalRTree: Creates an empty R-Tree with a specified number of children.
intFromDouble(Point3d, boolean) - Static method in class PointConverter: Convert a Point3d to a Point3i, optionally rounding values.
intFromDoubleCeil(Point3d) - Static method in class PointConverter: Convert a Point3d to a Point3i using the ceiling operation.
intFromDoubleFloor(Point2d) - Static method in class PointConverter: Convert a Point2d to a Point2i using the floor operation.
intFromDoubleFloor(Point3d) - Static method in class PointConverter: Convert a Point3d to a Point3i using the floor operation.
intFromFloat(Point3f, boolean) - Static method in class PointConverter: Convert a Point3f to a Point3i, optionally rounding values.
IntToFloatFunction - Interface in org.anchoranalysis.core.functional.unchecked: Represents a function that accepts an int-valued argument and produces a float-valued result.
INVALID_AXIS_INDEX - Static variable in class AxisConverter: Human-readable error message used when an invalid int-value for axis is passed.
INVALID_AXIS_STRING - Static variable in class AxisConverter: Human-readable error message used when an invalid String-value for axis is passed.
invalidate() - Method in interface FeatureCalculationCache: Invalidates existing caches so the next calculation occurs freshly.
invalidate() - Method in interface ResettableCalculation: Resets the cached-calculation, so the next call to doOperationWithParameters() is guaranteed to calculation the operation, and store the value in the cache.
invalidate() - Method in class CalculationPart
invalidate() - Method in class CalculationPartMap: Invalidates the cache, removing any items already stored.
invalidateExcept(Set<ChildCacheName>) - Method in interface FeatureCalculationCache: Invalidates existing caches so the next calculations occur freshly - except some particular child-caches who are not invalidated.
InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path.convert: An exception throw if an invalid-path is inputted as an argument.
InvalidPathArgumentException(String) - Constructor for exception InvalidPathArgumentException
InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception InvalidPathArgumentException
invert(Mask) - Static method in class MaskInverter: Modifies a mask so that off voxels become on voxels and vice versa.
invert() - Method in class BinaryVoxels: Changes the off state to be the on state and vice-versa.
invert() - Method in class BinaryValuesByte: Inverts the values so off becomes on, and vice-versa.
invert() - Method in class ObjectMask: Produces a new object-mask that uses the same voxel-buffer but switches the off and on mapping.
Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtracts each voxel from the maximum value for the channel's data type (e.g.
Invert() - Constructor for class Invert
Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Switches on voxels to off and vice-versa.
Invert() - Constructor for class Invert
Invert - Class in org.anchoranalysis.plugin.image.bean.scale: Invert the ScaleFactor calculated by the scaleCalculator delegate.
Invert() - Constructor for class Invert
Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a segmentation and inverts and on and off bytes
Invert() - Constructor for class Invert
invert() - Method in class ScaleFactor: Build a new scale factor where each dimension is set to the reciprocal of its current value.
InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
InvertedMax() - Constructor for class InvertedMax
invertObjectDuplicate(ObjectMask) - Static method in class MaskInverter: Creates a new object-mask where off voxels become on voxels and vice versa.
isAcceptDirectoryErrors() - Method in class SearchDirectory: If true, continues when a directory-access-error occurs (logging it), otherwise throws an exception.
isAccepted() - Method in class DualMarksAnnotation: Whether the the annotation was marked as accepted by the annotator?
isAccepted() - Method in class KernelDecision
isAccepted() - Method in class Reporting
isAcceptMissingResolution() - Method in class WithResolutionBase: Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
isAcceptMissingResolution() - Method in class VoxelPhysicalSize: Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
isAcceptNoResolution() - Method in class ReadVoxelExtentXml: If false, an exception is thrown if the resolution file is missing for a particular image.
isAcceptOutsideScene() - Method in class CheckMarkWithMask
isAddName() - Method in class CombineCSV
isAddOne() - Method in class Quantile
isAlways2D() - Method in class StackWriteAttributes: Whether the output is guaranteed to only ever 2D i.e.
isApplyResolution() - Method in class DistanceTransform3D: Multiples the values by the x-resolution, if it exists.
isApplyToPath() - Method in class MatchRegularExpression: If true, the filter is applied to the path as a whole, not just the filename (using forward slashes as directory separators)
isAsPercentage() - Method in class Quantile: If true, the quantile is interpreted as a percentage rather than a decimal
isAtLeastOnePositive() - Method in class MorphologicalIterations: Checks that at least one of iterationsDilation and iterationsErosion is more than 0
isAvoidBulletOnFirst() - Method in class SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
isAvoidDivideByZero() - Method in class Divide
isAvoidOverlappingObjects() - Method in class PairNeighbors: If true, no overlapping objects are treated as pairs
isBest() - Method in class Reporting
isBest() - Method in class VoxelizedMarksChangeReporter
isBigNeighborhood() - Method in class Dilate
isBigNeighborhood() - Method in class ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc.
isBigNeighborhood() - Method in class DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
isBigNeighborhood() - Method in class Dilate
isBigNeighborhood() - Method in class TraverseOuterContourOnImage
isBinary() - Method in class StackWriteAttributes: Whether all channels represent a binary image.
isBinary() - Method in class ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are ouputted.
isBit0() - Method in class RegionMembership
isBit1() - Method in class RegionMembership
isBit2() - Method in class RegionMembership
isBit3() - Method in class RegionMembership
isBit4() - Method in class RegionMembership
isBit5() - Method in class RegionMembership
isBit6() - Method in class RegionMembership
isBit7() - Method in class RegionMembership
isBold() - Method in class TextStyle: Whether to bold the drawn text
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderBase
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderXY
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderZ
isBufferOff(UnsignedByteBuffer) - Method in class KernelPointCursor: Is the value at the current index in this buffer corresponding to an off state?
isBufferOn(UnsignedByteBuffer) - Method in class KernelPointCursor: Is the value at the current index in this buffer corresponding to an on state?
isBySlices() - Method in class ConnectedComponentsFromMask
isCalledRegisterAllPackage() - Static method in class RegisterBeanFactories: Has the method RegisterBeanFactories.registerAllPackageBeanFactories() already been called?
isCaseSensitive() - Method in class PatternSpan: Iff true, a case sensitive search is used to match patterns.
isCellUsed(int, int) - Method in class TableItemArrangement
isChangeExisting() - Method in class ConvertBase: If true, the existing channel can be changed.
isClearOutsideMask() - Method in class ThresholdAgainstChannel
isCollapseFilename() - Method in class FilePathAppendBase
isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType: Can these parameters be used with a particular feature?
isCompatibleWith(Mark) - Method in interface CompatibleWithMark
isCompatibleWith(Mark) - Method in class AndList
isCompatibleWith(Mark) - Method in class CheckMarkWithMask
isCompatibleWith(Mark) - Method in class FeatureValueCheckMark
isCompatibleWith(Mark) - Method in class Not
isCompatibleWith(Mark) - Method in class RadiiMinRatio
isCompatibleWith(Mark) - Method in class VolumeMin
isCompatibleWith(Mark) - Method in class CreateNew
isCompatibleWith(Mark) - Method in class FromMarkProposer
isCompatibleWith(Mark) - Method in class FromObjects
isCompatibleWith(Mark) - Method in class FromProvider
isCompatibleWith(Mark) - Method in class FromSerializedMarks
isCompatibleWith(Mark) - Method in class Check
isCompatibleWith(Mark) - Method in class Check
isCompatibleWith(Mark) - Method in class MarkFromCollectionProposerUnary
isCompatibleWith(Mark) - Method in class UniformRandom
isCompatibleWith(Mark) - Method in class FromSerializedObject
isCompatibleWith(Mark) - Method in class MarkProposerFromList
isCompatibleWith(Mark) - Method in class MarkProposerReference
isCompatibleWith(Mark) - Method in class MarkProposerUnary
isCompatibleWith(Mark) - Method in class ObjectAsPoints
isCompatibleWith(Mark) - Method in class OrientationAndRadiiProposer
isCompatibleWith(Mark) - Method in class Position
isCompatibleWith(Mark) - Method in class MarkMergeProposerReference
isCompatibleWith(Mark) - Method in class MergeMarkEllipse
isCompatibleWith(Mark) - Method in class RandomOrientation
isCompatibleWith(Mark) - Method in class RandomXY
isCompatibleWith(Mark) - Method in class IncludeRandomObjects
isCompatibleWith(Mark) - Method in class XYOrientationExtendToZ
isCompatibleWith(Mark) - Method in class RadiiProposerRepeat
isCompatibleWith(Mark) - Method in class UniformRandomRadiiProposer
isCompatibleWith(Mark) - Method in class MarkSplitProposerReference
isCompatibleWith(Mark) - Method in class KernelBirthPartition
isCompatibleWith(Mark) - Method in class KernelReplacePartition
isCompatibleWith(Mark) - Method in class KernelBirthAndKill
isCompatibleWith(Mark) - Method in class KernelDeath
isCompatibleWith(Mark) - Method in class KernelExchange
isCompatibleWith(Mark) - Method in class KernelInitialMarksFromPartition
isCompatibleWith(Mark) - Method in class KernelInitialMarksProposed
isCompatibleWith(Mark) - Method in class KernelInitialMarksVoxelized
isCompatibleWith(Mark) - Method in class KernelMerge
isCompatibleWith(Mark) - Method in class KernelSplit
isCompatibleWith(Mark) - Method in class KernelBirthVoxelized
isCompatibleWith(Mark) - Method in class ConstantWeight
isCompatibleWith(Mark) - Method in class NumberPoints
isCompatibleWith(Mark) - Method in class FitPoints
isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipseFitter
isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipsoidFitter
isCompatibleWith(Mark) - Method in class Reference
isCompatibleWith(Mark) - Method in class ReflectInAxesWithinDistance
isCompleted() - Method in class JobState
isCompletedFailure() - Method in class JobState
isCompletedSuccessfully() - Method in class JobState
isConditionTrue() - Method in class DictionaryCondition
isConnectedComponentID(int) - Method in class EncodedIntBuffer
isConnectedComponentIDCode(int) - Method in class EncodedVoxels
isConnectedComponentIDCode(int) - Method in class WatershedEncoding
isConsiderForMerge() - Method in class PrioritisedVertex
isConvexHull() - Method in class FitPointsFromObjects: If true, Reduces the set of points by applying a convex-hull operation
isCopyNonInputs() - Method in class InputArguments: If True, any files in the input directory that are unused as inputs, are copied to the output directory.
isCov() - Method in class ObjectRadiusStandardDeviation
isCreateShort() - Method in class ArrangeRaster
isCreateShort() - Method in class GenerateString
isCreateShort() - Method in class TileWithLabels
isCreateShort() - Method in class DistanceTransform3D
isCreateShort() - Method in class DistanceTransformForEachObject3D
isCreateShort() - Method in class CreateNew: If True creates an unsigned short-image
isCsvIgnoreZeros() - Method in class ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
isDatasetNameSubdirectory() - Method in class ExperimentResultsExperimentStructure: If true the datasetName is appended as a subdirectory e.g.
isDay() - Method in class ExperimentIdentifierAuto: If true, the current day (yyyy.MM.dd) is included in the output
isDebug() - Method in class RootPath: If true this root is preferred, when executing a job in debugging mode.
isDebug() - Method in class ThresholdedFeature
isDebugEnabled() - Method in class InputOutputContextStateful
isDebugEnabled() - Method in interface InputOutputContext: Is debug-mode enabled?
isDebugEnabled() - Method in class OptimizationContext
isDebugMode() - Method in class PathPrefixerContext: Whether debug-mode is activated.
isDebugModeActivated() - Method in class InputManagerParameters
isDebugModeEnabled() - Method in class ExecutionArguments
isDefault() - Method in interface SelectParam: Is this the default option that occurs without any additional user effort?
isDefault() - Method in class UseDefaultManager
isDetailedLogging() - Method in class ExperimentFeedbackContext: Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
isDetailedLogging() - Method in class InputBound
isDetailedLogging() - Method in class ParametersExperiment: Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
isDifferentColorsForPairs() - Method in class AssignmentColorPool: If true, different colors are used for paired objects, otherwise always the same color is used.
isDirect() - Method in class UnsignedBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class VoxelBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class VoxelBufferUnsigned
isDirectionChainCode(int) - Method in class EncodedVoxels
isDirectionChainCode(int) - Method in class WatershedEncoding
isDisableDebugMode() - Method in class RootedFilePath
isDisableDebugMode() - Method in class Rooted
isDo3D() - Method in class AnisotropicDiffusion: Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
isDo3D() - Method in class ObjectCollectionProviderMorphological
isDo3D() - Method in class MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D
isDo3D() - Method in class PairNeighbors
isDo3D() - Method in class TouchingVoxels
isDo3D() - Method in class Erode
isDo3D() - Method in class NumberRemovedVoxelsAfterClosing
isDo3D() - Method in class OutlineKernelBase
isDo3D() - Method in class UniformRandomRadiiProposer
isDrawReverseLine() - Method in class Orientation
isDuplicate() - Method in class Reference: If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
isDuplicate() - Method in class Reference: If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
isEightBitChannels() - Method in class StackWriteAttributes: Whether each channel is 8 bits.
isEmpty() - Method in class DoubleList
isEmpty() - Method in class DoubleSet
isEmpty() - Method in class IntegerList
isEmpty() - Method in class IntegerSet
isEmpty() - Method in interface PrimitiveBeanCollection: Whether the collection is empty or not.
isEmpty() - Method in class StringList
isEmpty() - Method in class StringSet
isEmpty() - Method in class MapCreate: Whether the map is empty or not.
isEmpty() - Method in interface NamedProvider: Are there any items in the provider?
isEmpty() - Method in class RecordedExecutionTimes: Are there no recorded operations?
isEmpty() - Method in class FeatureList: Returns true if this list contains no elements.
isEmpty() - Method in class ResultsVectorList: Returns true if the list contains no elements.
isEmpty() - Method in class TimeSequence
isEmpty() - Method in class ObjectCollection: Whether the collection contains no objects.
isEmpty() - Method in class InputsWithDirectory
isEmpty() - Method in class RecordedOutputs: If no output-names exist.
isEmpty() - Method in class Histogram: If no value exists in the histogram with a count greater than zero.
isEmpty() - Method in class UpdatableMarksList
isEmpty() - Method in class MarkCollection
isEmpty() - Method in class Extent: Does the extent contain zero voxels?
isEmpty() - Method in class PointRange: Has a valid min and max defined?
isEmpty() - Method in class RTree: Returns true if and only if the R-tree is empty of entries.
isEnabled() - Method in class TextFileOutput
isErodeAtBoundary() - Method in class ConvexHullBase
isErrorDisconnectedObjects() - Method in class RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
isEvaluated() - Method in class CachedSupplierBase: Has the function already been evaluated?
isExceptionIfEmpty() - Method in class FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise is returned.
isExcludeZero() - Method in class Intensity: Iff true, zero-valued voxels are excluded from the histogram
isExcludeZero() - Method in class IntensityMeanMaxSlice
isExcludeZero() - Method in class Intensity: If true, zeros are excluded from considering in the histogram
isExecuting() - Method in class JobState
isExitBeforeOptimization() - Method in class SegmentWithMarkedPointProcess: Iff true the algorithm exits before optimization begins (useful for debugging).
isExitWithMinima() - Method in class WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
isExpandLabelZ() - Method in class TileWithLabels
isExtendInZ() - Method in class ExportObjectsAsCroppedImages: Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
isFieldAnnotatedAsOptional(Field) - Static method in class FieldAccessor: Is a particular Field on a AnchorBean marked as optional?
isFindMaxima() - Method in class ExtractSlice: If true, the maxima of the score is searched for.
isFinished() - Method in class DualMarksAnnotation
isFirst() - Method in class AsSingle: Iff true, first object is used, otherwise the second
isFirstDefined() - Method in class OutputEnableRulesSpecify
isFirstLineHeaders() - Method in class CombineCSV
isFixRandomSeed() - Method in class SegmentWithMarkedPointProcess: Iff true uses a constant seed for the random-number-generator (useful for debugging).
isFlatten() - Method in class MultipleComparer: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
isFlatten() - Method in class CompareAnnotations: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
isFlatten() - Method in class ExteriorContour: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
isFlatten() - Method in class ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced.
isForceChangeBytes() - Method in class Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
isForceDetailedLogging() - Method in class OutputExperiment: Whether more detailed log-messages around each experiment occur.
isForceEagerEvaluation() - Method in class NamedChannelsAppend
isForceRGB() - Method in class ArrangeRaster: If set, ensures every stack is converted into 3 channels
isForwardDirectionOnly() - Method in class XYOrientationExtendToZ
isGaussian() - Method in class AddEdgeFilters: If true, the Gaussian filter is included
isHighestTwoRadiiOnly() - Method in class RadiiRatio
isIgnoreAtThreshold() - Method in class OutlineKernelBase
isIgnoreCase() - Method in class FilePathPattern: if true, case is ignored in the pattern matching.
isIgnoreFileNotFoundAppend() - Method in class NamedChannelsAppend
isIgnoreFittingFailure() - Method in class FitPointsFromObjects: If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
isIgnoreHidden() - Method in class SearchDirectory: If true, case is ignored in the pattern matching.
isIgnoreHidden() - Method in class FilePathPattern: Iff true, any hidden-path is not considered, and simply ignored
isIgnoreHigherSide() - Method in class GaussianCumulative
isIgnoreLowerSide() - Method in class GaussianCumulative
isIgnoreMissingChannel() - Method in class IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
isIgnoreNaN() - Method in class Sum: If true, we ignore any NaN values.
isIgnoreNoObjects() - Method in class SegmentInstanceWithModel: If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
isIgnoreOutside() - Method in class KernelApplicationParameters: When true, any parts of the neighborhood that lie outside the scene are not considered in kernel neighborhoods.
isIgnoreOutside() - Method in enum OutsideKernelPolicy: When true, any parts of the neighborhood that lie outside the scene are not considered in kernel neighborhoods.
isIgnoreRangeAxisOutside() - Method in class LinePlot
isIgnoreZero() - Method in class RatioNonMode
isIgnoreZeros() - Method in class HistogramCSVGenerator: Iff true bins in the histogram with a zero count are not written
isIgnoreZIfNaN() - Method in class DistanceTransform3D: If the z-resolution is undefined, the z dimenion is ignored.
isIncludeBatchDimension() - Method in class SegmentObjectsFromONNXModel: If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
isIncludeDirectories() - Method in class DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
isIncludeFeatureNames() - Method in class EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
isIncludeFileName() - Method in class AppendDictionary
isIncludeFirst() - Method in class PairNeighbors: Include features for the First-object of the pair
isIncludeMerged() - Method in class PairNeighbors: Include features for the Merged-object of the pair
isIncludeSecond() - Method in class PairNeighbors: Include features for the Second-object of the pair
isIncludeShell() - Method in class MaxOverlapRatio
isIncludeZ() - Method in class Outline: If true the outline is also applied in the z-dimension, otherwise this is ignored as possible boundary
isIncludeZ() - Method in class NotTouchingSceneBorder
isInitialized() - Method in class InitializableBean: Has the been already been initialized via a call to InitializableBean.initialize(BeanInitialization, Logger) or similar.
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class JobProcessor: Is an input-object compatible with this particular task?
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class Task: Is an input-object compatible with this particular task?
isInteger() - Method in class FloatVoxelType
isInteger() - Method in class SignedVoxelType
isInteger() - Method in class UnsignedVoxelType
isInteger() - Method in class VoxelDataType: Whether the data-type represents an integer or floating-point?
isInterleaveChannels() - Method in class SegmentObjectsFromONNXModel: If true, the channels are placed as the final position of the tensor (**after** width/height) instead of **before** width/height.
isInterleaved() - Method in class ImageFileEncoding: Whether the channels are interleaved
isInterpolate() - Method in class AtScale
isInverse() - Method in class IntersectsWithContainer
isInverse() - Method in class IntensityMeanShellBase: Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
isInverseMask() - Method in class IntensityMeanShellBase: If true, uses the inverse of the passed mask.
isInvert() - Method in class MaskAsObject: If true the Mask is inverted before conversion into an ObjectCollection.
isInvert() - Method in class FromObjects
isInvert() - Method in class FilterWithRegularExpression: Iff true, then a file is rejected if the regular-expression matches and vice-versa.
isInvertDecisionValue() - Method in class FeatureListProviderSVMClassifier
isItemIncluded(T) - Method in class Plot: Whether to include this particular item in the plot?
isKeepEntireImage() - Method in class ExportObjectsAsCroppedImages: If true, rather than writing out a bounding-box around the object-mask, the entire image is written
isKeepExtremes() - Method in class Identity
isKeepZ() - Method in class ImposeResolution: Keep the z-resolution if it is already defined
isKeyRequired() - Method in class RegularExpression
isLabel() - Method in class MontageSlices: If true a label is added beside every image showing the slice index
isLeaf() - Method in class ErrorNodeImpl
isLocalized() - Method in class FilesProviderWithDirectoryString
isLogPath() - Method in class Rooted: if true, the pathIn and pathOut are logged.
isMarksSpan(MarkCollection) - Method in class RandomCollectionWithAddCriteria
isMarksSpan() - Method in class VoxelizedMarksWithEnergy
isMarksSpan(MarkCollection) - Method in class EnergySavedPairs
isMax() - Method in class IdentityImposeValueRelationToHistogram
isMedian() - Method in class AddEdgeFilters: If true, the median filter is included
isMemberFlag(byte, byte) - Method in class RegionMembership
isMemberFlag(byte, byte) - Method in class RegionMembershipAnd
isMemberFlag(byte, byte) - Method in class RegionMembershipOr
isMemberFlag(byte) - Method in class RegionMembershipWithFlags
isMemberFlagAnd(byte, byte) - Static method in class RegionMembershipUtilities
isMemberFlagOr(byte, byte) - Static method in class RegionMembershipUtilities
isMerge() - Method in class CutBelowThreshold
isMinima(int) - Method in class EncodedIntBuffer
isMinima(int) - Method in class EncodedVoxels
isMip() - Method in class NumberVoxels
isMip() - Method in class SurfaceNumberVoxelsBase
isMip() - Method in class OverlapMIPBase
isNoBlack() - Method in class ThresholderAutoIJ
isNormalize() - Method in class Identity
isNormalize() - Method in class BoundingBoxZOverlapRatio
isNormalizeFeatures() - Method in class FeatureListProviderSVMClassifier: Normalize features
isNoScale() - Method in class ScaleFactor: Does the scale-factor involve no scaling at all?
isNumeric() - Method in class TypedValue: Whether the value is numeric or not.
isNumeric() - Method in class ReportFeature
isNumeric() - Method in class ReportFeatureOnMark
isNumeric() - Method in class ReportFeatureOnMarks
isNumeric() - Method in class ReportFeatureOnObjectsBase
isNumeric() - Method in class ReportFeatureWrapError
isNumeric() - Method in class NumberMarksFromManifest
isNumeric() - Method in class ReportFeatureForManifestFileBase
isNumeric() - Method in class RootFilePathRegEx
isOff(int, int, int) - Method in interface BinaryOnOffSetter: Does the voxel at this point have an off state?
isOff(Point3i) - Method in interface BinaryOnOffSetter: Does the voxel at this point have an off state?
isOff(byte) - Method in class BinaryValuesByte: Does a particular value correspond to the off state?
isOmitExperimentIdentifier() - Method in class OutputArguments
isOmitExperimentIdentifier() - Method in class OutputPrefixerSettings: Requests that the experiment-identifier (name and index) is not included in the output-directory path.
isOn(int, int, int) - Method in interface BinaryOnOffSetter: Does the voxel at this point have an on state?
isOn(Point3i) - Method in interface BinaryOnOffSetter: Does the voxel at this point have an on state?
isOn(byte) - Method in class BinaryValuesByte: Does a particular value correspond to the on state?
isOn() - Method in interface OutputSequence
isOn() - Method in class OutputSequenceIncrementing
isOn() - Method in class OutputSequenceIndexed
isOpenInDesktop() - Method in class ExperimentExecutor: Whether to open the output directory in the desktop GUI after execution (if supported on the O/S).
isOperationAlreadyRecorded(String) - Method in class ExecutionTimeRecorder: Has a particular operation already been recorded?
isOperationAlreadyRecorded(String) - Method in class ExecutionTimeRecorderIgnore
isOutline() - Method in class ColoredBase: If true, an outline is drawn around the entries.
isOutlineAtBoundary() - Method in class ExteriorContour
isOutputEnabled() - Method in class CSVWriter
isOutputEnabled(String) - Method in class All
isOutputEnabled(String) - Method in class IgnoreUnderscorePrefix
isOutputEnabled(String) - Method in class None
isOutputEnabled(String) - Method in class SpecificDisabled
isOutputEnabled(String) - Method in class SpecificEnabled
isOutputEnabled(String) - Method in class MultiLevelBinary
isOutputEnabled(String) - Method in class MultiLevelNot
isOutputEnabled(String) - Method in class OutputEnabledMutable
isOutputEnabled(String) - Method in class SingleLevelBinary
isOutputEnabled(String) - Method in class SingleLevelInSet
isOutputEnabled(String) - Method in class SingleLevelNot
isOutputEnabled(String) - Method in interface SingleLevelOutputEnabled: Is a particular a particular output-enabled?
isOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings: Requests outputting with an incrementing number sequence, rather than the usual outputter (normally based upon input filenames).
isOutputShort() - Method in class GradientBase: Iff true, outputs a short channel, otherwise byte channel
isOutsideAtThreshold() - Method in class OutlineKernelBase
isOutsideOffUnignored() - Method in class KernelApplicationParameters: True only when voxels outside the scene should not be ignored and considered as off.
isOutsideOffUnignored() - Method in class KernelPointCursor: True only when voxels outside the scene should not be ignored and considered as off.
isOutsideOn() - Method in class KernelApplicationParameters: In cases where KernelApplicationParameters.isIgnoreOutside() is false, then whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOn() - Method in class KernelPointCursor: Whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOn() - Method in enum OutsideKernelPolicy: In cases where OutsideKernelPolicy.isIgnoreOutside() is false, then whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOnUnignored() - Method in class KernelApplicationParameters: True only when voxels outside the scene should not be ignored and considered as on.
isOverlappingObjects() - Method in class OutlinePreserveRelativeSize: Whether objects may overlap or not when unscaled.
isParamPrefixAppendNumber() - Method in class PermuteFirstSecondOrder: If true the constant is appended to the param prefix (a dot and a number)
isPhysical() - Method in class UnitConverter
isPlateau(int) - Method in class EncodedVoxels
isPlayloadUsed() - Method in class MergePairs
isPlayloadUsed() - Method in class MergeToIncreaseObjectFeature
isPlayloadUsed() - Method in class MergeWithFeature: Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class VisitSchedulerConvexAboutRoot
isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class VisitSchedulerConvexAboutRoot
isPointInside(Point3i) - Method in class Ellipse
isPointInside(Point3i) - Method in class Ellipsoid
isPointInside(Point3i) - Method in class MarkWithPositionAndSingleRadius
isPointInside(Point3i) - Method in class Mark
isPointInside(Point3i) - Method in class LineSegment
isPointInside(Point3i) - Method in class PointList
isPointInside(Point3i) - Method in class Polygon
isPointInside(Point3i) - Method in class PolygonCurve
isPointInside(Point3i) - Method in class RotatableBoundingBox
isPointInside(DrawOverlay, Point3i) - Method in class OverlayMark
isPointInside(DrawOverlay, Point3i) - Method in class OverlayObjectMask
isPointInside(DrawOverlay, Point3i) - Method in class Overlay: Is a point inside an overlay? (for a particular OverlayWriter).
isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class CheckMarkWithMask
isPrefix() - Method in class FromXMLList: If true, a prefix is prepended to the name of each added bean.
isPreserveAspectRatio() - Method in class FitTo: If true, the aspect-ratio is preserved between width and height.
isPreserveAspectRatio() - Method in class ToDimensions: If true, the ratio between x and y is kept constant when scaling.
isPreserveExtensionIfDuplicate() - Method in class RemoveExtension: Keeps the extension if the file-name (without the extension) becomes duplicated with another.
isPreserveSubdirectories() - Method in class ClusterByTimestamp: If true, the entire relative-path is used when copying files into the cluster directory.
isPrioritizeInputContext() - Method in class MatchExtensions: When true, any extensions available in the input-context are prioritized ahead of extensions.
isProposal() - Method in class VoxelizedMarksPeriodicReporter
isProposed() - Method in class KernelDecision
isRadiusInMeters() - Method in class WithRadiusBase
isReadFromResources() - Method in class SegmentObjectsFromONNXModel: When true, rather than reading modelPath from the file-system, it is read from Java resources on the class-path.
isRecordedAsEnabled(String) - Method in class RecordedOutputs: Is a particular output-name recorded as enabled?
isRecurseSubfolders() - Method in class MultiFileReader
isRecursive() - Method in class SearchDirectory: If true the search is applied recursively over sub-directories.
isRecursive() - Method in class ExperimentResultsExperimentStructure: Whether to apply the search recursively or not
isRejectIterationIfAllLow() - Method in class Erode
isRejectIterationIfDisconnected() - Method in class Erode
isRelativeForIdentifier() - Method in class InputArguments: If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.
isRelativeForIdentifier() - Method in class InputContextParameters: If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.
isRelativeToDirectory() - Method in class FileNamerContext: If true, the namer should prefer to derive file-names relative to the directory, rather than only the varying elements in the file-names.
isRemoveExtension() - Method in class FilePathPattern: if true, the extension is removed from paths before finding the pattern.
isRemoveExtensionInDescription() - Method in class LastDirectories: Whether to remove the file-extension from the filename.
isRemoveNaNColumns() - Method in class ExportFeaturesStyle: When true, columns containing all Double.NaN values are removed before outputting.
isRemoveNaNColumns() - Method in class FeatureExporterContext: When true, columns containing all Double.NaN values are removed before outputting.
isRemoveTouchingBorderXY() - Method in class FeatureCostAssigner
isReplaceMatchesWithSolids() - Method in class CompareAnnotations
isReplaceWithMidpoint() - Method in class MergeGreedyToIncreaseObjectFeature
isReportFitterErrors() - Method in class FitPoints
isRequireAllFilesMatch() - Method in class GroupFiles
isRequireBBoxNeighbors() - Method in class MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
isRequireTouching() - Method in class MergeWithFeature: Requires the object-masks to touch.
isResultUnusual(double) - Method in class ReplaceInfinity
isResultUnusual(double) - Method in class ReplaceNaN
isResultUnusual(double) - Method in class ReplaceUnusualValue
isRewardHigherSide() - Method in class GaussianCumulative: Treat the higher side as if it's the the fill cdf
isRewardLowerSide() - Method in class GaussianCumulative
isRGB() - Method in class DisplayStack: Does the display-stack contain an RGB image?
isRgb() - Method in class ImageMetadata: Whether the image is RGB or not.
isRGB() - Method in class Stack: If true, and the stack has exactly three channels, this stack can be interpreted as a RGB image.
isRGB() - Method in interface NamedChannelsForSeries: Whether the channels describe an RGB image.
isRGB() - Method in class NamedChannelsForSeriesConcatenate
isRGB() - Method in class NamedChannelsForSeriesMap
isRGB() - Method in interface OpenedImageFile: Whether the image-file has RGB encoded voxels.
isRGB() - Method in class ScaleableBackground
isRGB(IFormatReader) - Method in class Default
isRGB(IFormatReader) - Method in class ForceBitsPerPixel
isRGB(IFormatReader) - Method in class ForceNumberChannels
isRGB(IFormatReader) - Method in class ForceTimeSeriesToStack
isRGB(IFormatReader) - Method in class ReadOptions: Is it an image with three channels (red, green and blue)?
isRGB(IFormatReader) - Method in class ReadOptionsDelegate
isRGB(IFormatReader) - Method in class SwitchChannelTime
isRgb() - Method in class ImageFileEncoding: Whether the source bytes encoded as RGB (i.e.
isRgb() - Method in class FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one
isRGB() - Method in class OpenedMultiFile
isRootInStructure() - Method in class ExperimentResultsExperimentStructure: If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
isScaleLabel() - Method in class TileWithLabels
isSecond() - Method in class ExperimentIdentifierAuto: Only relevant if time==true.
isSecondary() - Method in class VoxelizedMarksPeriodicReporter: If proposal is true, this toggles between the primary and secondary proposal
isSelective() - Method in class OutputPattern: Whether the output should be checked to see if it is allowed or not.
isShowAgg() - Method in class MemoryUsageReporter
isShowBest() - Method in class MemoryUsageReporter
isShowDomainAxis() - Method in class BarPlot
isShowVerticalAxisLines() - Method in class PlotInstance
isShuffle() - Method in class InputArguments: If true, the order of the inputs are shuffled (randomized).
isShuffle() - Method in class InputContextParameters: If true, the order of the inputs are shuffled (randomized).
isSigmaInMeters() - Method in class BlurStrategy
isSilentlyDeleteExisting() - Method in class OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.
isSingleChannel() - Method in class StackWriteAttributes: The number of channels is guaranteed to be 1 in the output.
isSkipAtBorder() - Method in class FillHoles: If true we do not fill any objects that touch the border
isSkipFileName() - Method in class LastDirectories: Iff true the filename is not considered, only the subdirectories.
isSkipFileName() - Method in class FilePathAppendBase
isSkipMissingChannels() - Method in class NamedChannelsAppend
isSlicesSeparately() - Method in class FitBoxToOnVoxels
isStackAsChannel() - Method in class MultiInputManagerQuick: If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
isStackBackground() - Method in class VisualizeOnBackground
isStrongEdgeEnhancer() - Method in class AnisotropicDiffusion: If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.
isSubtractFromMaskOnly() - Method in class SubtractMean
isSuppress3D() - Method in class MorphologicalOperatorBase
isSuppress3D() - Method in class SurfaceNumberVoxelsBase
isSuppress3D() - Method in class SegmentThresholdAboveMinBound
isSuppressDirectories() - Method in class FromDescriptiveName: If true, any directory separators in the identifier in a descriptive-name are replaced by underscores.
isSuppressErrors() - Method in class ExportFeaturesStyle: When false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class FeatureCalculationContext: When false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class FeatureExporterContext: If false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class FromObjects: When true, exceptions aren't thrown when feature-calculations fail, but rather a log error message is written.
isSuppressExceptions() - Method in class JobProcessor
isSuppressExceptions() - Method in class ParametersUnbound
isSuppressExceptions() - Method in class QuickMultiDatasetExperiment
isSuppressExceptions() - Method in class QuickMultiDatasetStructuredExperiment
isSuppressOutlineZ() - Method in class ColoredBase: if true, the outline is suppressed in the z-dimension i.e.
isSuppressRes() - Method in class RadiiRatio
isSuppressRootOut() - Method in class Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
isSuppressSeries() - Method in class ConvertImageFormat: If true, the series index is not included in the outputted file-names.
isSuppressSubfolders() - Method in class DefineOutputter
isSuppressZ() - Method in class BoundingBoxIntersection
isSuppressZ() - Method in class DistanceTransform3D
isSuppressZ() - Method in class DistanceTransformForEachObject3D
isSuppressZ() - Method in class MergeWithOptionalDistanceConstraint
isSuppressZ() - Method in class CostOverlapWithinMidpointDistance
isSuppressZ() - Method in class ImageMomentsBase: If true co-voariance is suprpessed in z-dimension
isSuppressZ() - Method in class CenterOnMask
isSuppressZ() - Method in class UniformRandom
isSuppressZ() - Method in class SurfaceSizeMaskNonZero
isSuppressZ() - Method in class EllipsoidBase: Iff true, surpresses covariance in the z-direction.
isSuppressZCovariance() - Method in class FromObjects
isSuppressZCovariance() - Method in class LinearLeastSquaresEllipsoidFitter
isTemporary(int) - Method in class EncodedIntBuffer
isTemporary(int) - Method in class EncodedVoxels
isThreeChannels() - Method in class StackWriteAttributes: The number of channels is guaranteed to be 3 in the output.
isThrowExceptionForInsufficientPoints() - Method in class CreateMarkFromPoints
isThumbnailsEnabled() - Method in class FeatureCalculationContext
isTime() - Method in class ExperimentIdentifierAuto: If true, the current time (HH.mm.ss) is included in the output
isTransposed() - Method in class CombineCSV
isTrue(ObjectWithProperties, RGBStack, int) - Method in interface IfElse.Condition
isUnchanged(double, int) - Method in class UnchangedBase: Whether the current value is unchanged compared to the previous value.
isUnchanged(double, int) - Method in class UnchangedScore
isUnchanged(double, int) - Method in class UnchangedSize
isUniformlySized() - Method in class StackNotUniformSized: Do all channels have identical dimensions?
isUniformTyped() - Method in class StackNotUniformSized: Do all Channels in the stack have identical voxel data-type?
isUnsigned() - Method in class FloatVoxelType
isUnsigned() - Method in class SignedVoxelType
isUnsigned() - Method in class UnsignedVoxelType
isUnsigned() - Method in class VoxelDataType: Whether the data-type is unsigned?
isUnstarted() - Method in class JobState
isUnvisited(int) - Method in class EncodedIntBuffer
isUnvisited(int) - Method in class EncodedVoxels
isUseLastSeriesIndexOnly() - Method in class NamedChannels
isUseLastSeriesIndexOnly() - Method in class Stacks
isUseMax() - Method in class OverlapRatio
isUseMax() - Method in class OverlapRatioMask
isUseZ() - Method in class KernelApplicationParameters: Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
isUseZ() - Method in class KernelPointCursor: Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
isUseZ() - Method in class RemoveTouchingBorder
isUseZ() - Method in class TraverseOuterContourOnImage
isValidName(String, boolean) - Static method in class RGBChannelNames: Whether the channel-name is one of red, green, or blue, or alpha.
isValidNameSet(Set<String>) - Static method in class RGBChannelNames: Do the channel-names correspond exactly to those expected either RGB or RGBA.
isValidNameSet(Set<String>, boolean) - Static method in class RGBChannelNames: Do the channel-names correspond exactly to those expected for one of RGB or RGBA.
isVaryColors() - Method in class SegmentInstanceWithModel: If true the colors change for different objects in the image (using a default color set).
isVisuallyShortenDecimals() - Method in class ExportFeaturesStyle: When true, feature-values are shown as visually compressed as possible, including suppressing decimal places.
isVisuallyShortenDecimals() - Method in class FeatureExporterContext: When true double values are printed to be as short as possible without losing precision.
isVoxelOn(Point3i) - Method in class Mask: Does a particular voxel have the on state?
iterateEntries(CheckedBiConsumer<K, V, E>) - Method in class MapCreate: Iterate over each entry in the map, and apply an operation.
IterateKernelHelper - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines to iterate a Kernel over some or all of the voxels in a BinaryVoxels.
iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class FunctionalIterate: Iterate through all entries in a Map.
iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface SliceBufferIndex: Calls sliceConsumer once for each slice with the respective buffer.
iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface SliceBufferIndex: Calls process for each offset in each slice.
iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class Extent: Calls processor once for each x and y-values in the range.
iterateOverXY(PointTwoDimensionalConsumer) - Method in class Extent: Calls processor once for each x and y-values in the range.
iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class Extent: Calls processor once for each x and y-values but only passing an offset.
iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent: Calls processor once for each x and y-values in the range.
iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class Extent: Calls processor once for each x and y-values in the range, with a shift added.
iterateOverYXOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent: Calls processor once for each x and y-values in the range.
iterateOverZ(CheckedIntConsumer<E>) - Method in class Extent: Calls processor once for each z-value in the range.
iterateOverZUntil(IntPredicate) - Method in class Extent: Calls processor once for each z-value in the range unless indexPredicate returns false.
iterateValues(Histogram.BinConsumer) - Method in class Histogram: Calls consumer for every value, increasing from min to max.
iterateValuesUntil(int, Histogram.BinConsumer) - Method in class Histogram: Calls consumer for every value until a limit, increasing from min to limit.
IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over all voxels in one or more Voxels.
IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of image voxels within a bounding-box.
IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator: Like IterateVoxelsAll but specifically for equal-to operations on Voxels of type UnsignedByteBuffer.
IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but specifically for processing areas of intersection between BoundedVoxels of type UnsignedByteBuffer.
IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask: Utilities for iterating over the subset of voxels corresponding to an on state in a Mask.
IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Utilities for iterating over the neighboring voxels to a given point.
IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an ObjectMask.
IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an optional ObjectMask.
IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over remaining voxels in one or more VoxelBuffers.
iterator() - Method in class SequenceInteger: An iterator for each element in the sequence.
iterator() - Method in class DoubleList
iterator() - Method in class DoubleSet
iterator() - Method in class IntegerList
iterator() - Method in class IntegerSet
iterator() - Method in class StringList
iterator() - Method in class StringSet
iterator() - Method in class ColorList
iterator() - Method in class NameValueMap
iterator() - Method in class ConcurrentJobMonitor
iterator() - Method in class FeatureList
iterator() - Method in class CombinedName
iterator() - Method in class SimpleName
iterator() - Method in class FeatureNameList
iterator() - Method in class ResultsVectorList
iterator() - Method in class CacheTransferSourceCollection
iterator() - Method in class SharedFeatures
iterator() - Method in class NamedFeatureStore
iterator() - Method in class BoundingBoxesOnPlane
iterator() - Method in class ObjectCollectionWithProperties
iterator() - Method in class Stack
iterator() - Method in class StackNotUniformSized
iterator() - Method in class StackSeries
iterator() - Method in class TimeSequence
iterator() - Method in class ObjectCollection
iterator() - Method in class InputsWithDirectory
iterator() - Method in class EnergySavedInd
iterator() - Method in class EnergySchemeSet
iterator() - Method in class MemoList
iterator() - Method in class UpdatableMarksList
iterator() - Method in class ColoredMarks
iterator() - Method in class MarkCollection
iterator() - Method in class WeightedKernelList
iterator() - Method in class ColoredOverlayCollection
iterator() - Method in class OverlayCollection
iterator() - Method in class OverlayProperties
iterator() - Method in class ImageCounterList
iterator() - Method in class LevelResultCollection
iterator() - Method in class ParsedFilePathBag
iterator() - Method in class SortedSetChannel
iteratorCoupledManifests() - Method in class ManifestCouplingDefinition
iteratorCoupledManifestsFor(Manifest) - Method in class ManifestCouplingDefinition
iteratorExperimentalManifests() - Method in class ManifestCouplingDefinition
iteratorFromRaster() - Method in class NamedChannelsForSeriesConcatenate

J

JobDescription - Class in org.anchoranalysis.experiment.task.processor
JobDescription(String, int) - Constructor for class JobDescription
jobDirectory() - Static method in class DirectoryMatch
JobExecutionException - Exception in org.anchoranalysis.experiment: An exception that occurs when a job is executed.
JobExecutionException(String) - Constructor for exception JobExecutionException
JobExecutionException(Throwable) - Constructor for exception JobExecutionException
JobExecutionException(String, Throwable) - Constructor for exception JobExecutionException: A string message displayed to the user as well as a stack-trace of the cause
JobProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor: Processes a job
JobProcessor() - Constructor for class JobProcessor
JobRootDirectory - Class in org.anchoranalysis.io.manifest.directory: The root directory for where outputs for a particular experiment occur.
JobRootDirectory() - Constructor for class JobRootDirectory
JobStartStopLogger - Class in org.anchoranalysis.experiment.task.processor: Logs events when jobs start and stop, with or without errors.
JobStartStopLogger(String, ConcurrentJobMonitor, boolean, int, Optional<MessageLogger>) - Constructor for class JobStartStopLogger: Creates a job-logger.
JobState - Class in org.anchoranalysis.experiment.task.processor
JobState() - Constructor for class JobState
joinNonEmpty(String, String...) - Static method in class StringUtilities: Like String.join(java.lang.CharSequence, java.lang.CharSequence...) but ignores any empty strings, and returns Optional.empty() if all components are empty.
JoinRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an outstring of the form
JoinRegExGroups() - Constructor for class JoinRegExGroups
JPEG - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a JPEG file.
JPEG() - Constructor for class JPEG

K

Kernel - Class in org.anchoranalysis.image.voxel.kernel: A small matrix that is convolved with or otherwise combined across each voxel in an image.
Kernel(int) - Constructor for class Kernel: Creates a kernel with a given size in the X and Y dimensions.
Kernel<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.kernel: Modifies an entity by applying a kernel.
Kernel() - Constructor for class Kernel
kernelAccepted(Kernel<S, U>, Optional<T>, T, TransformationContext) - Method in interface KernelUpdater: Informs that a proposal from a particular kernel has been accepted
kernelAccepted(Kernel<S, U>, Optional<T>, T, TransformationContext) - Method in class KernelUpdaterSimple
KernelApplicationParameters - Class in org.anchoranalysis.image.voxel.kernel: Parameters used for applying a Kernel to a BinaryVoxels.
KernelApplicationParameters(OutsideKernelPolicy, boolean) - Constructor for class KernelApplicationParameters
KernelAssigner<S,T,U> - Interface in org.anchoranalysis.mpp.segment.optimization.kernel
kernelAssigner() - Method in class AssignMode
KernelAssignerAddErrorLevel<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
KernelAssignerAddErrorLevel(KernelAssigner<S, T, U>, ErrorNode) - Constructor for class KernelAssignerAddErrorLevel
KernelAssignerCalculateEnergyFromKernel<S,T,V> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
KernelAssignerCalculateEnergyFromKernel(KernelStateBridge<S, T>) - Constructor for class KernelAssignerCalculateEnergyFromKernel
KernelBirth<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent: Adds a new mark (a "birth") to create a proposal.
KernelBirth() - Constructor for class KernelBirth
KernelBirthAndKill - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelBirthAndKill() - Constructor for class KernelBirthAndKill
KernelBirthPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark: Proposes new marks ONLY if they haven't already been proposed and accepted.
KernelBirthPartition() - Constructor for class KernelBirthPartition
KernelBirthVoxelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized: As an example, this is like sampling with replacement.
KernelBirthVoxelized() - Constructor for class KernelBirthVoxelized
KernelBirthVoxelized(MarkProposer) - Constructor for class KernelBirthVoxelized
KernelCalculateEnergyException - Exception in org.anchoranalysis.mpp.segment.optimization.kernel
KernelCalculateEnergyException(String) - Constructor for exception KernelCalculateEnergyException
KernelCalculateEnergyException(String, Exception) - Constructor for exception KernelCalculateEnergyException
KernelCalculationContext - Class in org.anchoranalysis.mpp.segment.optimization.kernel
KernelCalculationContext(MarkFactoryContext, EnergyStack, EnergySchemeWithSharedFeatures, RandomNumberGenerator, ErrorNode) - Constructor for class KernelCalculationContext
KernelDeath<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelDeath() - Constructor for class KernelDeath
KernelDeath.MarkAnd<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelDeathPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
KernelDeathPartition() - Constructor for class KernelDeathPartition
KernelDeathVoxelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized
KernelDeathVoxelized() - Constructor for class KernelDeathVoxelized
KernelDecision - Class in org.anchoranalysis.mpp.segment.optimization.kernel: A description of the decision made to accept/reject a kernel at a particular time instance (index)
KernelDecision(KernelWithIdentifier<?, ?>, boolean, boolean, int[], long, int, ProposerFailureDescription) - Constructor for class KernelDecision
kernelDescription() - Method in class Reporting
KernelExchange - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelExchange() - Constructor for class KernelExchange
kernelIdentifier() - Method in class Reporting
KernelIndependent<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.kernel: A kernel that makes proposals independently of the current state.
KernelIndependent() - Constructor for class KernelIndependent
KernelInitialMarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelInitialMarksFromPartition() - Constructor for class KernelInitialMarksFromPartition
KernelInitialMarksProposed - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelInitialMarksProposed() - Constructor for class KernelInitialMarksProposed
KernelInitialMarksVoxelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelInitialMarksVoxelized(MarkCollectionProposer) - Constructor for class KernelInitialMarksVoxelized
KernelInitialMarksVoxelized() - Constructor for class KernelInitialMarksVoxelized
KernelIterDescriptionSerializerPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
KernelIterDescriptionSerializerPeriodicReporter() - Constructor for class KernelIterDescriptionSerializerPeriodicReporter
KernelMerge - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelMerge() - Constructor for class KernelMerge
KernelPointCursor - Class in org.anchoranalysis.image.voxel.kernel: A mutable context around determining whether a particular point should be on or off with a BinaryKernel.
KernelPointCursor(int, Point3i, Extent, BinaryValuesByte, KernelApplicationParameters) - Constructor for class KernelPointCursor: Creates to be focused around a particular point in the image.
KernelPosNeg<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.kernel
KernelPosNeg() - Constructor for class KernelPosNeg
KernelProposer<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.kernel
KernelProposer() - Constructor for class KernelProposer
KernelProposerOption<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.kernel
KernelProposerOption() - Constructor for class KernelProposerOption
KernelProposerOptionDual<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
KernelProposerOptionDual() - Constructor for class KernelProposerOptionDual
KernelProposerOptionSingle<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
KernelProposerOptionSingle() - Constructor for class KernelProposerOptionSingle
KernelProposerOptionSingle(Kernel<T, S>, double) - Constructor for class KernelProposerOptionSingle
KernelReplace<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelReplace() - Constructor for class KernelReplace
KernelReplacePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
KernelReplacePartition() - Constructor for class KernelReplacePartition
KernelSplit - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelSplit() - Constructor for class KernelSplit
KernelStateBridge<U,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: Transforms a kernel-to-state and vice versa.
KernelStateBridge() - Constructor for class KernelStateBridge
kernelStateBridge() - Method in class AssignMode
kernelStateBridge() - Method in class DirectAssignMode
kernelStateBridge() - Method in class TransformationAssignMode
KernelStateBridgeIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: No transformation occurs as Kernel and State are the same type
KernelStateBridgeIdentity() - Constructor for class KernelStateBridgeIdentity
KernelStateBridgePixelize<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: State derived from the kernel takes the form of ToPixelized<T>
KernelStateBridgePixelize() - Constructor for class KernelStateBridgePixelize
KernelStateBridgeTransformer<U,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
KernelStateBridgeTransformer() - Constructor for class KernelStateBridgeTransformer
kernelToState() - Method in class KernelStateBridge
kernelToState() - Method in class KernelStateBridgeIdentity
kernelToState() - Method in class KernelStateBridgePixelize
kernelToState() - Method in class KernelStateBridgeTransformer
KernelUpdater<S,T,U> - Interface in org.anchoranalysis.plugin.mpp.segment.kernel.updater
KernelUpdaterSimple<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.updater
KernelUpdaterSimple(U, WeightedKernelList<S, U>, StateTransformer<Optional<T>, Optional<S>>) - Constructor for class KernelUpdaterSimple
KernelWithIdentifier<T,S> - Class in org.anchoranalysis.mpp.segment.optimization.kernel
KernelWithIdentifier(Kernel<T, S>, int) - Constructor for class KernelWithIdentifier
keys() - Method in interface NamedProvider: Returns a set of keys associated with the provider.
keys() - Method in class NamedProviderBridge
keys() - Method in class NamedProviderCombine
keys() - Method in class NameValueMap
keys() - Method in class EagerEvaluationStore
keys() - Method in class LazyEvaluationStore
keys() - Method in class Dictionary: All keys existing in the dictionary.
keys() - Method in class SharedFeatures
keys() - Method in class NamedStacks
keys() - Method in class WrapStackAsTimeSequenceStore
keySet() - Method in class NamedEntries
keySet() - Method in class GroupedAnnotationLabels
kurtosis(Histogram) - Static method in class HistogramStatistics: Calculates the kurtosis of a distribution of values, represented by their histogram.
Kurtosis - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the kurtosis of all the values in the histogram.
Kurtosis() - Constructor for class Kurtosis

L

label(Logger) - Method in class AnnotationWithStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
labelElements(Channel, List<T>, Optional<Map<Integer, T>>) - Method in class LabelObjects: Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc.
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class BinaryClassifierImageLabeller
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class DescriptiveNameContainsImageLabeller
labelFor(ImageCSVLabellerInitialization, ProvidesStackInput, InputOutputContext) - Method in class ImageCSVLabeller
labelFor(T, ProvidesStackInput, InputOutputContext) - Method in class ImageLabeller: Determines a particular group-identifier for an input
labelFor(ImageLabellerStringMapInitialization<T>, ProvidesStackInput, InputOutputContext) - Method in class ImageLabellerStringMap
labelFor(ProvidesStackInput, InputOutputContext) - Method in class SharedStateFilteredImageOutput: Determines a particular group-identifier for an input
labelHeaders() - Method in class FeatureOutputMetadata: Headers for the CSV File
LabelHeaders - Class in org.anchoranalysis.feature.io.results: Headers in a CSV file for the non-results (i.e.
LabelHeaders(String[]) - Constructor for class LabelHeaders: Creates with only non-group headers
LabelHeaders(String[], String[]) - Constructor for class LabelHeaders
LabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature: Generates a list of header-names for columns unrelated to features (identifiers and groups)
LabelledResultsVector - Class in org.anchoranalysis.feature.io.results: Like a ResultsVector but additionally contains labels to describe the calculated results.
LabelledResultsVector(ResultsVector) - Constructor for class LabelledResultsVector: Creates with no additional labels, and no group.
LabelledResultsVector(Optional<MultiName>, ResultsVector) - Constructor for class LabelledResultsVector: Creates with no additional labels other than a group.
LabelledResultsVector(RowLabels, ResultsVector) - Constructor for class LabelledResultsVector
LabelledResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature: Like a ResultsVectorWithThumbnail but additionally contains labels to describe the calculated results.
LabelledResultsVectorWithThumbnail(RowLabels, ResultsVectorWithThumbnail) - Constructor for class LabelledResultsVectorWithThumbnail
LabelObjects<T> - Class in org.anchoranalysis.image.core.object.label: Writes a unique ID (successive integer IDs) for each elements's voxels into a channel, and 0 for background.
LabelObjects(Optional<UnaryOperator<T>>, Optional<Consumer<OverlappingObject<T>>>, Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class LabelObjects
LabelObjects(Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class LabelObjects
labels() - Method in class FileLabelMap
LabelsForInput - Interface in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates labels for a given input (and index).
LanguageUtilities - Class in org.anchoranalysis.core.value: Utility functions for pluralizing words in strings.
LastDirectories - Class in org.anchoranalysis.plugin.io.bean.file.namer: Derives a name by taking the filename together with optionally several subdirectories names.
LastDirectories(int) - Constructor for class LastDirectories: Creates for a particular number of subdirectories.
LastDirectories() - Constructor for class LastDirectories
LastDirectoryAsPrefix - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
LastDirectoryAsPrefix() - Constructor for class LastDirectoryAsPrefix
lastIndex(String) - Method in class SequenceMemory
lastIndexOf(Object) - Method in class UpdatableMarksList
Launch - Class in org.anchoranalysis.launcher: A command-line interface used for launching experiments
LauncherConfig - Class in org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
LauncherConfig() - Constructor for class LauncherConfig
LaunchInteractiveBrowser - Class in org.anchoranalysis.browser.launcher: Command-line application for launching the anchor GUI application, otherwise known as interactive-browser.
LazyEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store: Lazily delays evaluating items until when they are first retrieved.
LazyEvaluationStore(String) - Constructor for class LazyEvaluationStore
leftSize() - Method in class OverlappingObjects: The total number of objects in the left set.
length() - Method in class Tuple3d: The magnitude of the tuple.
LessThan - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is less than valueSecond.
LessThan() - Constructor for class LessThan
LessThanBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 < double2.
LessThanBean() - Constructor for class LessThanBean
LessThanEqualTo - Class in org.anchoranalysis.math.relation: Returns true iff valueFirst is less than or equal to valueSecond.
LessThanEqualTo() - Constructor for class LessThanEqualTo
LessThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation: A relation double1 <= double2.
LessThanEqualToBean() - Constructor for class LessThanEqualToBean
lessThanMaxX() - Method in class KernelPointCursor: Whether the current point is less than the image's extent in the X-dimension?
lessThanMaxY() - Method in class KernelPointCursor: Whether the current point is less than the image's extent in the Y-dimension?
LevelFromHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Calculates a level (a threshold-value) from a histogram.
LevelFromHistogram() - Constructor for class LevelFromHistogram
LevelPerObjectBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with a level calculated for each object variously
LevelPerObjectBase() - Constructor for class LevelPerObjectBase
LevelPerObjectIndependently - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
LevelPerObjectIndependently() - Constructor for class LevelPerObjectIndependently
LevelPerObjectNeighbors - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Calculates a threshold-level for each object collectively based on other objects
LevelPerObjectNeighbors() - Constructor for class LevelPerObjectNeighbors
LevelResult - Class in org.anchoranalysis.plugin.image.intensity.level
LevelResult(int, ObjectMask, Histogram) - Constructor for class LevelResult
LevelResultCollection - Class in org.anchoranalysis.plugin.image.intensity.level
LevelResultCollection() - Constructor for class LevelResultCollection
LevelResultCollectionFactory - Class in org.anchoranalysis.plugin.image.intensity.level
Limit - Class in org.anchoranalysis.plugin.io.bean.file.provider
Limit() - Constructor for class Limit
Limit<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Limits the number of input-objects to a certain hard-maximum
Limit() - Constructor for class Limit
LimitWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
LimitWithDirectory() - Constructor for class LimitWithDirectory
LinearLeastSquaresEllipseFitter - Class in org.anchoranalysis.plugin.points.bean.fitter: Fits a set of points to an ellipse using a linear least squares method.
LinearLeastSquaresEllipseFitter() - Constructor for class LinearLeastSquaresEllipseFitter
LinearLeastSquaresEllipsoidFitter - Class in org.anchoranalysis.plugin.points.bean.fitter: Fits an ellipsoid to points using a linear least squares approach
LinearLeastSquaresEllipsoidFitter() - Constructor for class LinearLeastSquaresEllipsoidFitter
LinearLeastSquaresViaNormalEquationBase - Class in org.anchoranalysis.plugin.points.bean.fitter
LinearLeastSquaresViaNormalEquationBase() - Constructor for class LinearLeastSquaresViaNormalEquationBase
LinePlot<T extends AssociatedIndex> - Class in org.anchoranalysis.plot.index: A line graph with 1 or more series, with an index on the x-axis.
LinePlot(String, String[], LinePlot.YValGetter<T>) - Constructor for class LinePlot
LinePlot.YValGetter<T> - Interface in org.anchoranalysis.plot.index
LineSegment - Class in org.anchoranalysis.mpp.mark.points
LineSegment(Point3i, Point3i) - Constructor for class LineSegment
LineSegment() - Constructor for class LineSegment
list() - Method in class BoundingBoxesOnPlane
list() - Method in class BoundedList: The collection of element with bounding-boxes.
ListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory: Factory for creating a List of beans.
ListBeanFactory(Function<List<T>, Object>) - Constructor for class ListBeanFactory
ListBeanFactory() - Constructor for class ListBeanFactory
listFor(Class<?>) - Method in class Define: Retrieves the list of elements associated with a grouping-root.
listFrom2i(Mask) - Static method in class PointsFromMask: All points that have on state in a Mask as a list with type Point2i.
listFrom2i(ObjectMask) - Static method in class PointsFromObject: A list of two-dimensional integer points from the entire object-mask.
listFrom3d(ObjectMask) - Static method in class PointsFromObject: A list of points from the entire object-mask as Point3d.
listFrom3i(Mask) - Static method in class PointsFromMask: All points that have on state in a Mask as a list with type Point3i.
listFrom3i(ObjectMask) - Static method in class PointsFromObject: A list of three-dimensional integer points from the entire object-mask.
listFromAllOutlines2i(ObjectCollection) - Static method in class PointsFromObject: A list of points as three-dimensional integers from the outline of all objects in a collection.
listFromOutline2i(ObjectMask) - Static method in class PointsFromObject: A list of points as three-dimensional integers from the outline of an object-mask
listFromOutline3i(ObjectMask) - Static method in class PointsFromObject: A list of points as Point3i from the outline of an object-mask.
listIterator() - Method in class InputsWithDirectory
listIterator() - Method in class UpdatableMarksList
listIterator(int) - Method in class UpdatableMarksList
ListWithThumbnails<T,S> - Class in org.anchoranalysis.plugin.image.feature.object: A list of items with an associated thumbnail-batch
ListWithThumbnails(List<T>) - Constructor for class ListWithThumbnails
ListWithThumbnails(List<T>, ThumbnailBatch<S>) - Constructor for class ListWithThumbnails
loadAsObjects(Path, Dimensions, boolean, Logger) - Method in class ComparableSource: Loads the source of elements from the file-system and converts to a ObjectCollection.
loadAsObjects(Path, Dimensions, boolean, Logger) - Method in class DualMarksAnnotationAsObjects
loadAsObjects(Path, Dimensions, boolean, Logger) - Method in class MarksAsObjects
loadAsObjects(Path, Dimensions, boolean, Logger) - Method in class MaskAsObject
loadAsObjects(Path, Dimensions, boolean, Logger) - Method in class Objects
loadBean(Path) - Static method in class BeanXMLLoader: Creates a bean by loading an XML description from the filesystem
loadBean(Path, String) - Static method in class BeanXMLLoader: Creates a bean by loading an XML description from the filesystem.
loadBeanAssociatedXml(Path, String) - Static method in class BeanXMLLoader: Creates a bean by loading an XML description from the filesystem.
loadBeanLocalized(Path, String) - Static method in class BeanXMLLoader: Creates a bean by loading an XML description from the filesystem.
localise(Path) - Method in class AnchorBean: Called once after the bean is created, localising the bean to a path on the filesystem.
localise(Path) - Method in class QuickMultiDatasetExperiment
localise(Path) - Method in class QuickMultiDatasetStructuredExperiment
LocalisedBeanException - Exception in org.anchoranalysis.bean.xml.exception: Combines a chain of many exceptions into a single exception, searching for an ultimate cause and incorporating the messages from the chain into a single unified message.
LocalisedBeanException(String, Throwable) - Constructor for exception LocalisedBeanException: Create with a message and a cause.
LocalSlices - Class in org.anchoranalysis.image.voxel.kernel: Caches a small number of slices around which we wish to work, so the memory is efficiently accessed.
LocalSlices(int, int, Voxels<UnsignedByteBuffer>) - Constructor for class LocalSlices: Create with focus around a particular slice.
log(String) - Method in interface MessageLogger: Logs a message.
log(String) - Method in class NullMessageLogger
log(String) - Method in class StatefulNullMessageLogger
log(String) - Method in class ConsoleMessageLogger
log(String) - Method in class FailureOnlyMessageLogger
log(String) - Method in class MessageLoggerIntoString
log(String) - Method in class MessageLoggerList
log(String) - Method in class TextFileMessageLogger
Log4JReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
Log4JReporter() - Constructor for class Log4JReporter
logConversionMessages(MessageLogger) - Method in class ConvertedInput: Logs any messages stored from from conversion.
logDescription() - Method in class GraphLogger
logEmptyLine() - Method in interface MessageLogger: Writes an empty line to the log file.
logEnd(JobDescription, JobState, boolean) - Method in class JobStartStopLogger: Performs logging for when a job ends.
logFormatted(String, Object...) - Method in interface MessageLogger: Logs a message, derived from a format-string.
logFormatted(String, Object...) - Method in class NullMessageLogger
logFormatted(String, Object...) - Method in class StatefulNullMessageLogger
logFormatted(String, Object...) - Method in class ConsoleMessageLogger
logFormatted(String, Object...) - Method in class FailureOnlyMessageLogger
logFormatted(String, Object...) - Method in class MessageLoggerIntoString
logFormatted(String, Object...) - Method in class MessageLoggerList
logFormatted(String, Object...) - Method in class TextFileMessageLogger
Logger - Class in org.anchoranalysis.core.log: A logging-mechanism for both messages and errors.
Logger(MessageLogger) - Constructor for class Logger: Constructs with an error-reporter that writes into the message logger.
Logger(MessageLogger, ErrorReporter) - Constructor for class Logger
logger() - Method in class ElementOutputter
loggerForMonitor(ParametersExperiment) - Method in class JobProcessor
LoggingDestination - Class in org.anchoranalysis.experiment.bean.log: The destination(s) to which log-messages are sent.
LoggingDestination() - Constructor for class LoggingDestination
LoggingFixture - Class in org.anchoranalysis.test: Fixtures to create loggers that don't output anything.
logGraphDescription() - Method in class MergeGraph
logMemoryUsage(String, MessageLogger) - Static method in class MemoryUtilities: Logs a message to logger describing current memory usage of the JVM.
logStart(JobDescription) - Method in class JobStartStopLogger: Performs logging for when a job starts.
LONG_OPTION_OUTPUT - Static variable in class CommandLineOptions: Changes output manager.
LONG_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class CommandLineOptions: Output console only.
LoopablePoints - Class in org.anchoranalysis.plugin.mpp.contour.path: A set of points that can be looped, so as to form a path that ends with the same point that it begins with....
LoopablePoints(List<Point3i>, Point3i) - Constructor for class LoopablePoints
loopPointsLeft() - Method in class LoopablePoints
loopPointsRight() - Method in class LoopablePoints
lowerCountExistsThan(int) - Method in class PredicateAtCorner
lowerCountExistsThan(int) - Method in class PredicateImplementation
lowerCountExistsThan(int) - Method in interface VoxelsPredicate: Whether the count is less than a particular threshold.
LRUCache<K,V> - Class in org.anchoranalysis.core.cache: A cache that discards items that haven't being used recently or frequently.
LRUCache(int, CheckedFunction<K, V, E>) - Constructor for class LRUCache: Constructor.

M

main(String[]) - Static method in class LaunchInteractiveBrowser: Entry point for command-line application
main(String[]) - Static method in class Launch: Entry point for command-line application.
makeCopy(Path, Path) - Method in class CopyFilesMethod: Makes a copy of the file at source at destination.
makeCopyWithDirectory(Path, Path) - Method in class Bytewise
makeCopyWithDirectory(Path, Path) - Method in class CompressAnyTIFF
makeCopyWithDirectory(Path, Path) - Method in class CopyFilesMethod: Like CopyFilesMethod.makeCopy(Path,Path) but after any necessary directories are created so destination can be written.
makeOutputPath(String) - Method in class OutputterChecked: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makeOutputPath(Optional<String>, String, String) - Method in class OutputterChecked: Like OutputterChecked.makeOutputPath(String) but additionally adds an extension.
makeOutputPath(Optional<String>, String, String) - Method in class ElementOutputter: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makePathAbsolute(Optional<String>, Optional<String>, String) - Method in class DirectoryWithPrefix
makePathAbsolute(Optional<String>, Optional<String>, String) - Method in interface PathCreator: Generates a full path, given the final part (suffix) of a path.
makePathRelative(Path) - Method in class DirectoryWithPrefix
makePathRelative(Path) - Method in interface PathCreator: Extracts a relative-file path, given the final part (suffix) of a path.
makeProposal(Optional<T>, KernelCalculationContext) - Method in class Kernel: Calculates the Energy for a proposal
makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class KernelReplacePartition
makeProposal(Optional<T>, KernelCalculationContext) - Method in class KernelBirth
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class KernelBirthAndKill
makeProposal(Optional<T>, KernelCalculationContext) - Method in class KernelDeath
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class KernelExchange
makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class KernelInitialMarksFromPartition
makeProposal(Optional<MarkCollection>, KernelCalculationContext) - Method in class KernelInitialMarksProposed
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class KernelInitialMarksVoxelized
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class KernelMerge
makeProposal(Optional<T>, KernelCalculationContext) - Method in class KernelReplace
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class KernelSplit
makeRGBStack(Stack, boolean) - Static method in class ConvertToMat: Derives a Mat representing an RGB stack.
makeSureConfigured() - Method in class ConfigureBioformatsLogging: Makes sure logging is configured
Manifest - Class in org.anchoranalysis.io.manifest: A manifest that records what outputs occur and where they occur.
Manifest() - Constructor for class Manifest
MANIFEST_DESCRIPTION - Static variable in class ObjectCollectionWriter
MANIFEST_FUNCTION - Static variable in class NamedStacksOutputter
MANIFEST_FUNCTION - Static variable in class CSVReporterAggregated
MANIFEST_FUNCTION - Static variable in class CSVReporterBest
MANIFEST_FUNCTION_DICTIONARY - Static variable in class EnergyStackWriter
MANIFEST_FUNCTION_STACK - Static variable in class EnergyStackWriter
manifestCouplingDefinition(InputManagerParameters) - Method in class CoupledManifestsInputManager
ManifestCouplingDefinition - Class in org.anchoranalysis.plugin.io.manifest
ManifestCouplingDefinition() - Constructor for class ManifestCouplingDefinition
ManifestDescription - Class in org.anchoranalysis.io.manifest: A description of an entry (e.g.
ManifestDescription(String, String) - Constructor for class ManifestDescription
ManifestDeserializer - Interface in org.anchoranalysis.io.manifest.deserializer
ManifestDirectoryDescription - Class in org.anchoranalysis.io.manifest: A description of an directory in the manifest.
ManifestDirectoryDescription(Optional<ManifestDescription>, SequenceType<?>) - Constructor for class ManifestDirectoryDescription
ManifestDirectoryDescription(String, String, SequenceType<?>) - Constructor for class ManifestDirectoryDescription
ManifestGenerator - Class in org.anchoranalysis.io.generator.combined
ManifestGenerator() - Constructor for class ManifestGenerator
map(Stream<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class CheckedStream: Performs a Stream.map(java.util.function.Function<? super T, ? extends R>) but accepts a function that can throw a checked-exception.
map(Optional<S>, CheckedFunction<S, T, E>) - Static method in class OptionalUtilities: Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
map(CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class FeatureList: Creates a new feature-list where each feature is the result of applying a map-function to an existing feature.
map(UnaryOperator<ObjectMask>) - Method in class ObjectWithProperties: Maps the underlying object-mask to another object-mask, reusing the same properties object.
map(CheckedFunction<ObjectMask, ObjectMask, E>) - Method in class ObjectMaskStream: Creates a new ObjectCollection after mapping each item to another.
map(Function<T, S>) - Method in class InputsWithDirectory: Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
map(CheckedFunction<T, S, E>, Progress) - Method in class InputsWithDirectory: Like {InputsWithDirectory.map(Function) but increments a Progress.
mapBoth(Optional, Optional<V>, CheckedBiFunction<U, V, T, E>) - Static method in class OptionalUtilities: Mapping only occurs if both Optionals are non-empty (equivalent to a logical and on the optionals)
mapBoundingBoxChangeExtent(BoundingBox) - Method in class ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value).
mapBoundingBoxChangeExtent(BoundingBox) - Method in class ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
mapBoundingBoxPreserveExtent(BoundingBox) - Method in class BoundedVoxels: Applies a function to map the bounding-box to a new-value.
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).
mapCalculator(UnaryOperator<FeatureCalculatorMulti<T>>) - Method in class NamedFeatureCalculatorMulti
mapChannel(CheckedUnaryOperator<Channel, OperationFailedException>) - Method in class Stack: Produces a new stack with a particular mapping applied to each channel.
mapChannelIfSupported(int, BiFunction<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>, T>, Function<Channel, T>) - Method in class ChannelMapper: Maps a Channel with mapFunction if a corresponding converter exists, otherwise with fallback.
mapChannelWithIndex(CheckedBiFunction<Channel, Integer, Channel, OperationFailedException>) - Method in class Stack: Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).
MapCreate<K,V> - Class in org.anchoranalysis.core.identifier.name: A tree map that creates a new item, if it doesn't already exist upon a get operation.
MapCreate(Supplier<V>) - Constructor for class MapCreate: Creates without a comparator, using instead the natural ordering of elements.
MapCreate(Supplier<V>, Comparator<K>) - Constructor for class MapCreate: Creates with an explicit comparator.
mapFrom(Iterable<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class FeatureListFactory: Creates a new feature-list by mapping an Iterable to Feature
mapFrom(Iterable<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by mapping an Iterable to ObjectMask.
mapFromFiltered(Iterable<S>, Predicate<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class FeatureListFactory: Creates a new feature-list by filtering an iterable and then mapping it to a feature
mapFromOptional(Iterable<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by mapping an Iterable to Optional.
mapFromOptional(Iterator<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by mapping an Iterator to Optional.
mapFromRange(int, int, IntFunction<Feature<T>>) - Static method in class FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to a feature
mapFromRange(int, int, IntFunction<ObjectMask>) - Static method in class ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask.
mapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectMask, E>) - Static method in class ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask.
mapFromRangeOptional(int, int, Class<? extends Exception>, CheckedIntFunction<Optional<Feature<T>>, E>) - Static method in class FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to an optional feature
MapGroupToRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv: Maps Group (String) to a CSVRow
MapGroupToRow() - Constructor for class MapGroupToRow
mapIdentifier(BiFunction<String, File, String>) - Method in class NamedFile: Immutably renames the file, by assigning it a new identifier.
mapIntStream(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class CheckedStream: Creates a new feature-list by mapping integers (from a range) each to an optional feature accepting a checked-exception
mapList(List<S>, Progress, CheckedFunction<S, T, E>) - Static method in class FunctionalProgress: Maps a list to new list, updating a progress-reporter for every element.
mapListOptional(List<S>, Progress, CheckedFunction<S, Optional<T>, E>) - Static method in class FunctionalProgress: Maps a list to a new list, including only certain items, updating a progress-reporter for every element.
mapRangeToList(int, int, IntFunction<T>) - Static method in class FunctionalList: Creates a list of elements, where each element corresponds to an index in a range.
mapToInt(Stream<S>, Class<? extends Exception>, CheckedToIntFunction<S, E>) - Static method in class CheckedStream: Performs a Stream.mapToInt(java.util.function.ToIntFunction<? super T>) but accepts a function that can throw a checked-exception.
mapToList(Stream<S>, Function<S, T>) - Static method in class FunctionalList: Maps a stream to a list with each element derived from a corresponding element in the original collection.
mapToList(Collection<S>, Function<S, T>) - Static method in class FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection.
mapToList(Collection<S>, Collection, BiFunction<S, U, T>) - Static method in class FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection, as well as a corresponding argument from a second list.
mapToList(S[], Function<S, T>) - Static method in class FunctionalList: Maps an array to a list with each element derived from a corresponding element in the original array.
mapToList(Collection<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class FunctionalList: Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(S[], Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class FunctionalList: Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(CheckedFunction<ObjectMask, T, E>) - Method in class ObjectMaskStream: Creates a new List after mapping each item to another type.
mapToListOptional(Collection<S>, Function<S, Optional<T>>) - Static method in class FunctionalList: Maps a collection to a list with each element in the original collection maybe producing an element in the output.
mapToListOptional(Collection<S>, Class<? extends Exception>, CheckedFunction<S, Optional<T>, E>) - Static method in class FunctionalList: Maps a collection to a list with each element in the original collection maybe producing an element in the output.
mapToListOptional(CheckedFunction<ObjectMask, Optional<T>, E>) - Method in class ObjectMaskStream: Creates a new List after mapping each item to another (optional) type
mapToListWithIndex(List<S>, BiFunction<S, Integer, T>) - Static method in class FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection - and also letting the map function use an index.
mapToObj(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class CheckedStream: Performs a IntStream.mapToObj(java.util.function.IntFunction<? extends U>) but accepts a function that can throw a checked-exception.
mapToSortedSet(CheckedFunction<ObjectMask, T, E>) - Method in class ObjectMaskStream: Creates a new SortedSet after mapping each item to another type.
Mark - Class in org.anchoranalysis.mpp.mark
Mark(Mark) - Constructor for class Mark: Copy constructor
Mark() - Constructor for class Mark
MarkAnd(S, T) - Constructor for class KernelDeath.MarkAnd
markAsCompleted(boolean) - Method in class JobState
markAsExecuting() - Method in class JobState
markAsTemporary(int) - Method in class EncodedIntBuffer
MarkBounds - Class in org.anchoranalysis.mpp.bean.bound
MarkBounds() - Constructor for class MarkBounds
markBounds() - Method in class MarksInitialization
MarkBoundsDefine - Class in org.anchoranalysis.plugin.mpp.bean.bound
MarkBoundsDefine() - Constructor for class MarkBoundsDefine
MarkBoundsDefine(MarkBounds) - Constructor for class MarkBoundsDefine
MarkBoundsProvider - Class in org.anchoranalysis.mpp.bean.provider
MarkBoundsProvider() - Constructor for class MarkBoundsProvider
MarkBoundsReference - Class in org.anchoranalysis.plugin.mpp.bean.bound
MarkBoundsReference() - Constructor for class MarkBoundsReference
MarkCollection - Class in org.anchoranalysis.mpp.mark: An ordered collection of Marks.
MarkCollection() - Constructor for class MarkCollection: Creates with no elements in the collection.
MarkCollection(Stream) - Constructor for class MarkCollection: Creates from a stream of Marks.
MarkCollection(Mark) - Constructor for class MarkCollection: Creates from a single Mark.
MarkCollection(List) - Constructor for class MarkCollection
MarkCollectionDeserializer - Class in org.anchoranalysis.mpp.io.marks
MarkCollectionDeserializer() - Constructor for class MarkCollectionDeserializer
MarkCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer: Proposes an entire collection (confguration) of marks
MarkCollectionProposer() - Constructor for class MarkCollectionProposer
markCollectionProposers() - Method in class MarksInitialization
MarkCollectionProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides a collection of marks
MarkCollectionProvider() - Constructor for class MarkCollectionProvider
MarkConicFactory - Class in org.anchoranalysis.mpp.mark.conic
MarkEllipseCircumEstimate - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region: Estimates the circumference of an ellipse based upon finding the area of the shell, and dividing // by the shell
MarkEllipseCircumEstimate() - Constructor for class MarkEllipseCircumEstimate
MarkEllipseFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkEllipseFactory() - Constructor for class MarkEllipseFactory
MarkEllipsoidFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkEllipsoidFactory() - Constructor for class MarkEllipsoidFactory
MarkEvaluator - Class in org.anchoranalysis.mpp.feature.bean.mark
MarkEvaluator() - Constructor for class MarkEvaluator
MarkFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkFactory() - Constructor for class MarkFactory
MarkFactoryContext - Class in org.anchoranalysis.mpp.segment.optimization.kernel
MarkFactoryContext(MarkWithIdentifierFactory) - Constructor for class MarkFactoryContext
markFactoryContext() - Method in class OptimizationContext
MarkFromCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkFromCollectionProposer() - Constructor for class MarkFromCollectionProposer
MarkFromCollectionProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
MarkFromCollectionProposerUnary() - Constructor for class MarkFromCollectionProposerUnary
MarkMergeProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkMergeProposer() - Constructor for class MarkMergeProposer
MarkMergeProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
MarkMergeProposerReference() - Constructor for class MarkMergeProposerReference
markMergeProposers() - Method in class MarksInitialization
markNoProposal(ProposerFailureDescription) - Method in class OptimizationStep
MarkPairCollection - Class in org.anchoranalysis.mpp.feature.mark: A pair collection where the underlying type is a simple IdentifiablePair
MarkPairCollection() - Constructor for class MarkPairCollection
markPairs() - Method in class MarksInitialization
MarkPointListFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkPointListFactory() - Constructor for class MarkPointListFactory
MarkProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkProposer() - Constructor for class MarkProposer
MarkProposerFromList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
MarkProposerFromList() - Constructor for class MarkProposerFromList
MarkProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
MarkProposerReference() - Constructor for class MarkProposerReference
markProposers() - Method in class MarksInitialization
MarkProposerStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Annotates each image with a mark
MarkProposerStrategy() - Constructor for class MarkProposerStrategy
MarkProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
MarkProposerUnary() - Constructor for class MarkProposerUnary
MarkRegion - Class in org.anchoranalysis.mpp.bean.mark
MarkRegion() - Constructor for class MarkRegion
marks() - Method in interface AnnotationWithMarks: The marks associated with the annotation
marks() - Method in class DualMarksAnnotation
marks() - Method in class MarksInitialization
marks() - Method in class MultiInput
MARKS - Static variable in class OutputterDirectories: Where collections of marks are typically placed in a define-experiment output
MarksAsObjects - Class in org.anchoranalysis.plugin.annotation.bean.comparer: Loads a MarkCollection to compared, converting each Mark into an ObjectMask.
MarksAsObjects() - Constructor for class MarksAsObjects
MarksAsUniqueValueGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
MarksAsUniqueValueGenerator(Dimensions, RegionMembershipWithFlags) - Constructor for class MarksAsUniqueValueGenerator
marksAt(Point3i, RegionMap, int) - Method in class MarkCollection
MarksBaseProvider<T,S> - Class in org.anchoranalysis.mpp.bean.provider: Base class for MarksBean that implements Provider to provide an object of type S.
MarksBaseProvider() - Constructor for class MarksBaseProvider
MarksBean<T> - Class in org.anchoranalysis.mpp.bean
MarksBean() - Constructor for class MarksBean
marksDeriver() - Method in class MarkProposerStrategy
MarksFlattenedGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
MarksFlattenedGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class MarksFlattenedGenerator
MarksFromEnergyHelper - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
marksFromMemo(EnergyMemoList) - Static method in class MarksFromEnergyHelper
marksFromOverlays(OverlayCollection) - Static method in class OverlayCollectionMarkFactory
marksFromOverlays(ColoredOverlayCollection) - Static method in class OverlayCollectionMarkFactory
MarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.optimization: A subset of a marks (as extracted during a partition).
MarksFromPartition(MarkCollection, PartitionedMarks) - Constructor for class MarksFromPartition
MarksGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
MarksGenerator(DrawObject, IdentifierGetter<Overlay>) - Constructor for class MarksGenerator
MarksGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class MarksGenerator
MarksGeneratorBase - Class in org.anchoranalysis.mpp.io.marks.generator
MarksGeneratorBase(DrawOverlay, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class MarksGeneratorBase
MarksInitialization - Class in org.anchoranalysis.mpp.init
MarksInitialization(ImageInitialization) - Constructor for class MarksInitialization
MarksInitializationFactory - Class in org.anchoranalysis.mpp.io.input
marksNew() - Method in class KernelBirth
MarkSplitProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkSplitProposer() - Constructor for class MarkSplitProposer
MarkSplitProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
MarkSplitProposerReference() - Constructor for class MarkSplitProposerReference
markSplitProposers() - Method in class MarksInitialization
MarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
MarksWithDisplayStack(MarkCollection, DisplayStack) - Constructor for class MarksWithDisplayStack
MarksWithEnergyBreakdown - Class in org.anchoranalysis.mpp.feature.energy.marks: Marks with both the total energy and a breakdown by clique
MarksWithEnergyBreakdown(MarksWithTotalEnergy) - Constructor for class MarksWithEnergyBreakdown
MarksWithEnergyBreakdown(MarksWithTotalEnergy, EnergySavedInd, EnergySavedPairs, EnergySavedAll) - Constructor for class MarksWithEnergyBreakdown
MarksWithTotalEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks: A collection of marks with an associated (total) energy.
MarksWithTotalEnergy(MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class MarksWithTotalEnergy
MarkToObjectConverter - Class in org.anchoranalysis.mpp.mark: Converts a confidence-associated Mark to an equivalent ObjectMask.
MarkToObjectConverter(Dimensions) - Constructor for class MarkToObjectConverter: Create for particular Dimensions without a scaling-factor.
MarkToObjectConverter(Optional<ScaleFactor>, Dimensions) - Constructor for class MarkToObjectConverter: Create for particular Dimensions with a scaling-factor.
MarkToObjectConverter(Optional<ScaleFactor>, Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Constructor for class MarkToObjectConverter
MarkWithIdentifierFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkWithIdentifierFactory(MarkFactory) - Constructor for class MarkWithIdentifierFactory
MarkWithIdentifierFactory() - Constructor for class MarkWithIdentifierFactory
MarkWithPosition - Class in org.anchoranalysis.mpp.mark
MarkWithPosition() - Constructor for class MarkWithPosition
MarkWithPosition(MarkWithPosition) - Constructor for class MarkWithPosition
MarkWithPositionAndSingleRadius - Class in org.anchoranalysis.mpp.mark.conic: Base-class for a conic that has a single radius (circle, sphere etc.)
MarkWithPositionAndSingleRadius(Bound) - Constructor for class MarkWithPositionAndSingleRadius: Constructor with a bound on the radius
MarkWithPositionAndSingleRadius(MarkWithPositionAndSingleRadius) - Constructor for class MarkWithPositionAndSingleRadius: Copy constructor
MarkWithPositionAndSingleRadius() - Constructor for class MarkWithPositionAndSingleRadius
Mask - Class in org.anchoranalysis.image.core.mask: A channel whose voxel-values are restricted to two states (on and off).
Mask(Channel) - Constructor for class Mask: Creates a mask from an existing channel using default values for off (0) and on (255).
Mask(Channel, BinaryValuesInt) - Constructor for class Mask: Creates a mask from an existing channel.
Mask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class Mask: Creates a mask from an existing binary-voxels using default image resolution.
Mask(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>) - Constructor for class Mask: Creates a mask from an existing binary-voxels and a specific image resolution.
Mask(Dimensions, BinaryValuesInt) - Constructor for class Mask: Creates a new empty mask of particular dimensions and with particular BinaryValuesInt.
mask(String) - Static method in class ReferenceFactory
MaskAnd - Class in org.anchoranalysis.image.core.mask.combine: Performs a logical and operation on corresponding voxels in two Masks.
MaskAsObject - Class in org.anchoranalysis.plugin.annotation.bean.comparer: Loads Mask to compared, converting it into an ObjectMask.
MaskAsObject() - Constructor for class MaskAsObject
MaskAsSingleObject<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculate a feature, treating a mask as a single-object on the energy-stack
MaskAsSingleObject() - Constructor for class MaskAsSingleObject
MaskFactory - Class in org.anchoranalysis.image.core.mask: Helper routines to create new instances of Mask.
MaskFromObjects - Class in org.anchoranalysis.image.core.mask: Creates a Mask from one or more ObjectMasks.
MaskIntersectionAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner: No outputs are produced.
MaskIntersectionAssigner() - Constructor for class MaskIntersectionAssigner
MaskInverter - Class in org.anchoranalysis.image.core.mask: Inverts masks and objects.
MaskOr - Class in org.anchoranalysis.image.core.mask.combine: Performs a logical or operation on corresponding voxels in two Masks.
MaskProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Mask and associated Stack.
MaskProvider() - Constructor for class MaskProvider
MaskProviderUnary - Class in org.anchoranalysis.image.bean.provider
MaskProviderUnary() - Constructor for class MaskProviderUnary
MaskReader - Class in org.anchoranalysis.image.io.stack.input: Utility functions for reading a Mask from the file-system.
masks() - Method in class ImageInitialization
MaskXor - Class in org.anchoranalysis.image.core.mask.combine: Performs a logical xor (exclusive or) operation on corresponding voxels in two Masks.
match(String) - Method in class RegEx: Returns an array of string components it matches successfully, or Optional.empty() if it cannot match.
match(String) - Method in class RegExList
match(String) - Method in class RegExSimple
match(int, int) - Method in class HungarianAlgorithm: Helper method to record a matching between worker w and job j.
match(ObjectMask, Optional<Dimensions>) - Method in class DiscardOutliers
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class RelationWithMatches
match(ObjectMask, Optional<Dimensions>) - Method in class GreaterIntersectionWith
match(ObjectMask, Optional<Dimensions>) - Method in class IntensityGreaterEqualThan
match(ObjectMask, Optional<Dimensions>) - Method in class IntersectsWith
match(ObjectMask, Optional<Dimensions>) - Method in class NotTouchingSceneBorder
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class ThresholdedFeature
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class ThresholdedVolume
match(ObjectMask, Optional<Dimensions>) - Method in class ObjectFilterPredicate: A predicate condition for an object to be kept in the collection
match(ObjectMask, Optional<Dimensions>) - Method in class ObjectFilterRelation
match(ObjectMask, Optional<Dimensions>, DoubleBiPredicate) - Method in class ObjectFilterRelation
Match - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Match() - Constructor for class Match
match(String, ZoneOffset) - Method in class TimestampPattern: Matches certain times.
matchDirectories() - Method in class FinderSingleDirectory
MatchedAppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: An append CSV and corresponding match value
MatchedAppendCsv() - Constructor for class MatchedAppendCsv
MatchedObject - Class in org.anchoranalysis.image.core.object: An object with associated matches.
MatchedObject(ObjectMask, ObjectCollection) - Constructor for class MatchedObject
MatcherIntersectionHelper - Class in org.anchoranalysis.plugin.image.bean.object.match
matches(Path) - Method in interface FileFormat: Does a filePath (or fileName) have an extension expected by this format?
matches(String) - Method in interface FileFormat: Does a file-path (or file-name) end with an extension expected by this format?
matches(String, String) - Static method in class FormatExtensions: Does a filePath match an extension?
matches(String) - Method in enum ImageFileFormat
matches(String) - Method in enum NonImageFileFormat
matchesIdentifier(String) - Method in interface FileFormat: Does an identifier equal the extension expected by this format?
matchesIdentifier(String) - Method in enum ImageFileFormat
matchesIdentifier(String) - Method in enum NonImageFileFormat
MatchExtensions - Class in org.anchoranalysis.io.input.bean.path.matcher: Maybe imposes a file-extension condition, optionally on top of an existing matcher.
MatchExtensions(String) - Constructor for class MatchExtensions: Create for specific extension.
MatchExtensions() - Constructor for class MatchExtensions
MatchGlob - Class in org.anchoranalysis.io.input.bean.path.matcher
MatchGlob() - Constructor for class MatchGlob
MatchGlob(String) - Constructor for class MatchGlob
matchingFiles(Path, boolean, boolean, boolean, Optional<Integer>, Optional<InputManagerParameters>) - Method in class PathMatcher: Finds a collection of files that match particular conditions on their paths.
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class FilesProviderWithDirectory
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class FilesProviderWithDirectoryUnary
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class SearchDirectory
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class SingleFile
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class FileSetFromStringSet
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class DirectoryDepth
matchIntersectingObjects(ObjectCollection, ObjectCollection) - Static method in class MatcherIntersectionHelper
MatchRegularExpression - Class in org.anchoranalysis.io.input.bean.path.matcher: Predicates that matches a file-path against a regular expression.
MatchRegularExpression() - Constructor for class MatchRegularExpression
max(StackRGBState) - Method in enum StackRGBState: Finds the maximum of this value and another, according to an ordering.
max() - Method in class RunningSumExtrema: The maximum across all values passed to RunningSumExtrema.add(double) or Double.MIN_VALUE if the method was never called.
Max - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Max() - Constructor for class Max
max(double) - Method in class Point3d: Element-wise maximum between this point and a scalar.
max(Tuple3d) - Method in class Point3d: Element-wise maximum between this point and another.
max(ReadableTuple3i) - Method in class Tuple3i: Element-wise maximum between this point and another.
max(int) - Method in class Tuple3i: Element-wise maximum between this point and a scalar.
MAX_VALUE - Static variable in class FloatVoxelType: Minimum supported value for the type.
MAX_VALUE - Static variable in class SignedShortVoxelType: Maximum supported value for the type.
MAX_VALUE - Static variable in class UnsignedByteVoxelType: Minimum supported value for the type, as a long.
MAX_VALUE - Static variable in class UnsignedIntVoxelType: Maximum supported value for the type.
MAX_VALUE - Static variable in class UnsignedShortVoxelType: Minimum supported value for the type, as a long.
MAX_VALUE - Static variable in class ChainCodesDirection
MAX_VALUE_INT - Static variable in class UnsignedByteVoxelType: Maximum supported value for the type, as an int.
MAX_VALUE_INT - Static variable in class UnsignedShortVoxelType: Maximum supported value for the type, as an int.
maxAsInt(ToIntFunction<ObjectMask>) - Method in class ObjectMaskStream: Finds the maximum value of a function applied to each object in the collection.
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class VisitScheduler
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class VisitSchedulerAnd
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class VisitSchedulerConvexAboutRoot
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class VisitSchedulerMaxDistanceAlongContour
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class VisitSchedulerUniformSample
maxDistanceToClosestPoint(ContiguousVoxelPath, Point3i) - Static method in class DistanceToContiguousPath: The maximum-distance of a point to the closest point on the path
maxDistanceToHeadTail(ContiguousVoxelPath, Point3i) - Static method in class DistanceToContiguousPath
MaxFeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MaxFeatureIntersectingObjects() - Constructor for class MaxFeatureIntersectingObjects
Maximum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Maximum() - Constructor for class Maximum
Maximum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
Maximum() - Constructor for class Maximum
MaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
MaximumIntensityProjection() - Constructor for class MaximumIntensityProjection
MaximumNumberContourVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels on any slice's contour (edge voxels) across all slices.
MaximumNumberContourVoxelsOnSlice() - Constructor for class MaximumNumberContourVoxelsOnSlice
MaximumNumberVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels in the object-mask across all slices.
MaximumNumberVoxelsOnSlice() - Constructor for class MaximumNumberVoxelsOnSlice
MaxIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a Channel to UnsignedByteBuffer by scaling against the maximum intensity value that appears in it.
MaxIntensity() - Constructor for class MaxIntensity: Default constructor.
MaxIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a Channel to UnsignedByteBuffer by scaling against the maximum intensity value from a corresponding histogram.
MaxIntensityFromHistogram() - Constructor for class MaxIntensityFromHistogram: Default constructor.
MaxIntensityProjection - Class in org.anchoranalysis.image.voxel.buffer.max: Creates buffers for performing a Maximum Intensity Projection.
MaxIntensityProjectionPair - Class in org.anchoranalysis.plugin.mpp.feature.overlap
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, RegionMembershipWithFlags, RegionMembershipWithFlags) - Constructor for class MaxIntensityProjectionPair
MaxNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
MaxNonZero() - Constructor for class MaxNonZero
MaxOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
MaxOverlapRatio(double) - Constructor for class MaxOverlapRatio
MaxOverlapRatio() - Constructor for class MaxOverlapRatio
MaxRatioRadii - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
MaxRatioRadii() - Constructor for class MaxRatioRadii
MaxSliceArea - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
MaxSliceArea() - Constructor for class MaxSliceArea
MaxTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MaxTwoChannels(IntBinaryOperation) - Constructor for class MaxTwoChannels
maxValue() - Method in class VoxelDataType: The maximum value this type can represent.
MaxWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MaxWithConstant() - Constructor for class MaxWithConstant
MaxWithConstant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
MaxWithConstant() - Constructor for class MaxWithConstant
maybeAddPointToClosestEnd(Point3i) - Method in class ContiguousVoxelPath: Adds the point to the closest end of the path....
maybeAlways2D(boolean) - Static method in class StackWriteAttributesFactory: Creates a StackWriteAttributes which depending on a flag will always be 2D.
maybeCreateUserFriendlyException(Throwable) - Static method in class FriendlyExceptionCreator: Possibly replaces an exception with a more user-friendly description
maybeDistanceCondition() - Method in class MergeWithOptionalDistanceConstraint
maybeRGB(boolean, boolean, boolean) - Static method in class StackWriteAttributesFactory
maybeRGBWithoutAlpha(boolean) - Static method in class StackWriteAttributesFactory
maybeSubdirectory(Optional<String>, ManifestDirectoryDescription, boolean) - Method in interface InputOutputContext: Optionally creates a new context like with InputOutputContext.subdirectory(java.lang.String, org.anchoranalysis.io.manifest.ManifestDirectoryDescription, boolean) but only if a directory-name is defined
maybeSuppressDirectories(String, boolean) - Method in class OutputPrefixerSettings: Derives an identifier that maybe has its directories suppressed.
Mean - Class in org.anchoranalysis.feature.bean.results: The mean of the results from a particular feature.
Mean() - Constructor for class Mean
Mean - Class in org.anchoranalysis.image.feature.bean.histogram
Mean() - Constructor for class Mean
mean() - Method in interface VoxelStatistics: The mean of all voxel values.
mean() - Method in class RunningSum: Calculates the mean.
mean(double) - Method in class RunningSum: Calculates the mean.
mean() - Method in class RunningSumExtrema: Calculates the mean.
mean() - Method in class Histogram: Calculates the mean of the histogram values, considering their frequency.
mean(double) - Method in class Histogram: Calculates the mean of the values in the distribution, if each value is raised to a power.
mean(double, double) - Method in class Histogram: Like Histogram.mean(double) but a value may be subtracted before raising to a power.
mean() - Method in class VarianceCalculatorDouble: Calculate the mean, based on the current state of running-sums.
mean() - Method in class VarianceCalculatorLong: Calculate the mean, based on the current state of running-sums.
Mean<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list: Arithmetic mean of a list of features
Mean() - Constructor for class Mean
mean() - Method in class RunningSumPoint: The mean value of all points added to the running-sum, separately for all three-dimensions.
MeanAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the mean of a feature applied to each connected component
MeanAcrossObjects() - Constructor for class MeanAcrossObjects
meanAndReset() - Method in class RunningSum: Calculate the mean and then reset to zero.
meanAndReset() - Method in class RunningSumCollection: Calculate the mean of each item and reset to zero.
meanExecutionTimeFailed() - Method in class TaskStatistics: Mean execution-time of failed jobs in milliseconds.
meanExecutionTimeSeconds() - Method in class RecordedExecutionTimes.RecordedOperation: The mean execution time in seconds for the operation.
meanExecutionTimeSuccess() - Method in class TaskStatistics: Mean execution-time of successfully-completed jobs in milliseconds.
MeanFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
MeanFilter2D() - Constructor for class MeanFilter2D
MeanFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
MeanFromAll() - Constructor for class MeanFromAll
MeanGeometric<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
MeanGeometric() - Constructor for class MeanGeometric
MeanIntensityDifference - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
MeanIntensityDifference() - Constructor for class MeanIntensityDifference
MeanIntensityDifference(double) - Constructor for class MeanIntensityDifference
MeanIntensityProjection - Class in org.anchoranalysis.image.voxel.buffer.mean: Creates buffers for performing a mean-intensity-projection.
MeanIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
MeanIntensityProjection() - Constructor for class MeanIntensityProjection
MeanRaisedToPower - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the mean value in a histogram, and raises it to a power.
MeanRaisedToPower() - Constructor for class MeanRaisedToPower
MeanScale - Class in org.anchoranalysis.math.statistics: Stores the mean and scale for a distribution.
MeanScale(double, double) - Constructor for class MeanScale
MeanScale() - Constructor for class MeanScale
MeanThreeChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel that is the mean of three input channels
MeanThreeChannels() - Constructor for class MeanThreeChannels
meanXY() - Method in class RunningSumPoint: The mean value of all points added to the running-sum, only for the X- and Y-dimensions.
measureTime(boolean, String...) - Method in class ExecutionTimeRecorder: Indicates operationIdentifier is being recorded, and returns the current clock timestamp.
measureTime(boolean, String...) - Method in class ExecutionTimeRecorderIgnore
Median - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Applies a median-filter with square kernel
Median() - Constructor for class Median
Median - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Median() - Constructor for class Median
MedianFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
MedianFilter2D() - Constructor for class MedianFilter2D
MedianFilter3D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
MedianFilter3D() - Constructor for class MedianFilter3D
membershipForIndex(int) - Method in class RegionMap
membershipWithFlagsForIndex(int) - Method in class RegionMap
MemoForIndex - Interface in org.anchoranalysis.mpp.mark.voxelized.memo
MemoList - Class in org.anchoranalysis.mpp.feature.mark
MemoList() - Constructor for class MemoList
MemoryUsageReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
MemoryUsageReporter() - Constructor for class MemoryUsageReporter
MemoryUtilities - Class in org.anchoranalysis.core.system: Logs a message about approximate memory (RAM) usage of the JVM.
merge(ObjectMask, ObjectMask) - Static method in class ObjectMaskMerger: Merges two objects together.
merge(ObjectCollection) - Static method in class ObjectMaskMerger: Merges all the objects together that are found in a collection.
merge(TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class MergeGraph
merge() - Method in class MergeCandidate: Merges
merge(Stream<BoundingBox>) - Static method in class BoundingBoxMerger: Merges all the bounding boxes in a stream.
MergeBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: A base class for algorithms that merge object-masks.
MergeBase() - Constructor for class MergeBase
MergeBase.MergeObjects - Interface in org.anchoranalysis.plugin.image.bean.object.provider.merge
mergeBoundingBoxes(ObjectCollection) - Static method in class ObjectMaskMerger: Merges all the bounding boxes of a collection of objects.
mergeBoundingBoxes(Stream<ObjectMask>) - Static method in class ObjectMaskMerger: Merges all the bounding boxes of a stream of objects.
MergeCandidate - Class in org.anchoranalysis.plugin.mpp.contour.path.merge.strategy: Maintains two paths, and their closest point
MergeCandidate(ContiguousVoxelPath, ContiguousVoxelPath, Point3i, Point3i) - Constructor for class MergeCandidate
Merged - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates the first-object in a pair only
Merged(Feature<FeatureInputSingleObject>) - Constructor for class Merged
Merged() - Constructor for class Merged
MergedPairsFeatures - Class in org.anchoranalysis.image.feature.calculator.merged: The list of features that can be used in a PairsTableCalculator
MergedPairsFeatures(FeatureList<FeatureInputPairObjects>) - Constructor for class MergedPairsFeatures: Creates to only calculate pair features.
MergedPairsFeatures(FeatureList<FeatureInputStack>, FeatureList<FeatureInputSingleObject>, FeatureList<FeatureInputPairObjects>) - Constructor for class MergedPairsFeatures: Creates with features for single, pair and image as a whole.
MergedPairsInclude - Class in org.anchoranalysis.image.feature.calculator.merged
MergedPairsInclude() - Constructor for class MergedPairsInclude
MergedPairsInclude(boolean, boolean, boolean) - Constructor for class MergedPairsInclude
MergeGraph - Class in org.anchoranalysis.plugin.image.object.merge: A graph that stores each object as a vertex, where edges represent a neighborhood relation.
MergeGraph(PayloadCalculator, UpdatableBeforeCondition, Optional<UnitConverter>, AssignPriority, Logger, boolean) - Constructor for class MergeGraph: Constructor
MergeGreedyToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
MergeGreedyToIncreaseObjectFeature() - Constructor for class MergeGreedyToIncreaseObjectFeature
MergeLists - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
MergeLists() - Constructor for class MergeLists
MergeMarkEllipse - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
MergeMarkEllipse() - Constructor for class MergeMarkEllipse
mergeMultiplex(ObjectCollection, MergeBase.MergeObjects) - Method in class MergeBase: Merges either in a container, or altogether
mergeObjects(ObjectCollection) - Method in interface MergeBase.MergeObjects
MergePairs - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges objects if a pair feature value satisfies a condition.
MergePairs() - Constructor for class MergePairs
MergeSpatialClusters - Class in org.anchoranalysis.plugin.ml.bean.cluster: Merges spatially-adjacent objects using the DBScan clustering algorithm.
MergeSpatialClusters() - Constructor for class MergeSpatialClusters
MergeStrategy - Class in org.anchoranalysis.plugin.mpp.contour.path.merge.strategy
MergeStrategy(int) - Constructor for class MergeStrategy
MergeToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object.
MergeToIncreaseObjectFeature() - Constructor for class MergeToIncreaseObjectFeature
MergeTwoCollectionsItemwise - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges itemwise objects from two collections.
MergeTwoCollectionsItemwise() - Constructor for class MergeTwoCollectionsItemwise
mergeVertices(V, V, V) - Method in class GraphWithoutPayload: Merges two existing vertices together.
mergeViaZeroCheck(Channel, Channel, VoxelDataType, double) - Static method in class IfVoxelZero: Creates a new channel which is a merged version of two input channels according to rules.
MergeWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Base class for object-merging strategies that involve calculating a feature.
MergeWithFeature() - Constructor for class MergeWithFeature
MergeWithOptionalDistanceConstraint - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.
MergeWithOptionalDistanceConstraint() - Constructor for class MergeWithOptionalDistanceConstraint
messageLogger() - Method in class Logger: Where messages are logged to.
MessageLogger - Interface in org.anchoranalysis.core.log: Logs messages (strings) somewhere.
MessageLoggerIntoString - Class in org.anchoranalysis.experiment.log: Logs error messages into a String via StringBuilder.
MessageLoggerIntoString(StringBuilder) - Constructor for class MessageLoggerIntoString
MessageLoggerList - Class in org.anchoranalysis.experiment.log
MessageLoggerList(Stream<StatefulMessageLogger>) - Constructor for class MessageLoggerList
metadata(int, Logger) - Method in class NamedChannelsInput: The image-metadata associated with a particular series.
metadata() - Method in class ImageMetadataInput: The associated image metadata.
metadata(int, Logger) - Method in interface OpenedImageFile: Extracts metadata about the image.
metadataAggregated(NamedFeatureStore<FeatureInputResults>) - Method in class FeatureOutputMetadata: Derives metadata for the aggregated CSV output, if enabled.
metadataNonAggregated() - Method in class FeatureOutputMetadata: Derives metadata for the non-aggregated CSV output.
Midpoint - Class in org.anchoranalysis.image.io.bean.object.draw: Writes a cross at the midpoint of an object
Midpoint() - Constructor for class Midpoint
Midpoint(int) - Constructor for class Midpoint
midpoint() - Method in class BoundingBox: A mid-point in the bounding box, corresponding to the exact half-way point between (corner+extent)/2.
min(StackRGBState) - Method in enum StackRGBState: Finds the minimum of this value and another, according to an ordering.
min() - Method in class RunningSumExtrema: The minimum across all values passed to RunningSumExtrema.add(double) or Double.MAX_VALUE if the method was never called.
Min - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Min() - Constructor for class Min
min(Tuple3d) - Method in class Point3d: Element-wise minimum between this point and another.
min(ReadableTuple3i) - Method in class Point3d: Element-wise minimum between this point and another.
min(ReadableTuple3i) - Method in class Tuple3i: Element-wise minimum between this point and another.
MIN_VALUE - Static variable in class FloatVoxelType: Maximum supported value for the type.
MIN_VALUE - Static variable in class SignedShortVoxelType: Minimum supported value for the type.
minArea() - Method in class MaxIntensityProjectionPair
minAsInt(ToIntFunction<ObjectMask>) - Method in class ObjectMaskStream: Finds the minimum value of a function applied to each object in the collection.
minDistanceMaxToHeadTail(Point3i, List<ContiguousVoxelPath>) - Static method in class FindMinimumDistance: The maximum-distance of a point to the closest contiguous-path
MinFeatureAsIndividual - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
MinFeatureAsIndividual() - Constructor for class MinFeatureAsIndividual
MinFeatureIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MinFeatureIntersectingObjectsAboveThreshold() - Constructor for class MinFeatureIntersectingObjectsAboveThreshold
MinimaImposition - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
MinimaImposition() - Constructor for class MinimaImposition
MinimaImpositionGrayscaleReconstruction - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
MinimaImpositionGrayscaleReconstruction() - Constructor for class MinimaImpositionGrayscaleReconstruction
MinimalExecutionTimeStatsReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
MinimalExecutionTimeStatsReporter() - Constructor for class MinimalExecutionTimeStatsReporter
Minimum - Class in org.anchoranalysis.image.feature.bean.object.pair: Ratio of first-object to second-object in a pair
Minimum(Feature<FeatureInputSingleObject>) - Constructor for class Minimum
Minimum() - Constructor for class Minimum
Minimum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Minimum() - Constructor for class Minimum
Minimum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
Minimum() - Constructor for class Minimum
minimum(Extent) - Method in class Extent: An extent that contains the minimum of two extents for each dimension respectively.
minimumDimension() - Method in class ScaleFactor: Which is the minimum scaling-factor among all dimensions?
MinimumDistanceByDimension - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: The minimum distance in any one particular axis-aligned direction (i.e.
MinimumDistanceByDimension() - Constructor for class MinimumDistanceByDimension
MinimumFilter - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
MinimumFilter() - Constructor for class MinimumFilter
MinimumXYResolution - Class in org.anchoranalysis.plugin.image.bean.scale
MinimumXYResolution() - Constructor for class MinimumXYResolution
minNumPoints() - Method in class LinearLeastSquaresViaNormalEquationBase
MinTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MinTwoChannels(IntBinaryOperation) - Constructor for class MinTwoChannels
minVal - Variable in class FeatureValueCheckMark
minValue() - Method in class VoxelDataType: The minimum value this type can represent.
MinWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MinWithConstant() - Constructor for class MinWithConstant
MockFeatureWithCalculation - Class in org.anchoranalysis.test.feature.plugins.mockfeature: A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
MockFeatureWithCalculation() - Constructor for class MockFeatureWithCalculation
MockFeatureWithCalculationFixture - Class in org.anchoranalysis.test.feature.plugins.mockfeature: Creates a mock-feature which used a mock CalculationPart under the hood
Mode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Calculates the skewness of all the values in the histogram.
Mode() - Constructor for class Mode
MonitoredSequentialExecutor<T> - Class in org.anchoranalysis.experiment.task.processor: Runs executes sequence of jobs/tasks/whatever monitoring various pieces of information - how many have run? - how many successful/failed? - how long did execution take? - etc.
MonitoredSequentialExecutor(Predicate<T>, Function<T, String>, Optional<MessageLogger>, boolean) - Constructor for class MonitoredSequentialExecutor
MontageSlices - Class in org.anchoranalysis.plugin.imagej.bean.stack.provider
MontageSlices() - Constructor for class MontageSlices
moreThanOneObject() - Method in class AnnotationComparisonAssigner: Can more than one object exist?
moreThanOneObject() - Method in class FeatureCostAssigner
moreThanOneObject() - Method in class MaskIntersectionAssigner
MorphologicalDilation - Class in org.anchoranalysis.image.voxel.object.morphological: Performs morphological dilation on an ObjectMask or BinaryVoxels.
MorphologicalErosion - Class in org.anchoranalysis.image.voxel.object.morphological: Performs morphological erosion operation on an ObjectMask or BinaryVoxels.
MorphologicalIterations - Class in org.anchoranalysis.plugin.image.feature.bean.morphological: Specifies a certain number of iterations of the morphological operations of dilation and erosion
MorphologicalIterations() - Constructor for class MorphologicalIterations
MorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider: Applies an ImageJ (2D) morphological operation to each slice
MorphologicalOperation() - Constructor for class MorphologicalOperation
MorphologicalOperatorBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Base class for performing morphological operations on BinaryVoxels.
MorphologicalOperatorBase() - Constructor for class MorphologicalOperatorBase
moveAcceptedToAvailable(Mark) - Method in class PartitionedMarks
moveAvailableToAccepted(Set) - Method in class PartitionedMarks
MovieFromSlices - Class in org.anchoranalysis.plugin.image.task.bean.slice
MovieFromSlices() - Constructor for class MovieFromSlices
Mser - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies the MSER algorithm from imglib2
Mser() - Constructor for class Mser
MultiBufferSized - Class in org.anchoranalysis.plugin.io.multifile.buffer
MultiBufferSized(Stack, SizeExtents) - Constructor for class MultiBufferSized
MultiFileReader - Class in org.anchoranalysis.plugin.io.bean.stack.reader
MultiFileReader() - Constructor for class MultiFileReader
MultiInput - Class in org.anchoranalysis.mpp.io.input: An input to an experiment that combines a particular Stack with other types of entities.
MultiInput(ProvidesStackInput) - Constructor for class MultiInput
MultiInput(String, ProvidesStackInput) - Constructor for class MultiInput
MultiInputManager - Class in org.anchoranalysis.mpp.io.bean.input
MultiInputManager(String, InputManager<? extends ProvidesStackInput>) - Constructor for class MultiInputManager
MultiInputManager() - Constructor for class MultiInputManager
MultiInputManagerQuick - Class in org.anchoranalysis.plugin.quick.bean.input: A multi-input manager that makes various assumptions, so it can be more quickly specified.
MultiInputManagerQuick() - Constructor for class MultiInputManagerQuick
MultiInputSubMap<T> - Interface in org.anchoranalysis.mpp.io.input: A sub-item of a MultiInput.
MultiLevelAnd - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in both of two MultiLevelOutputEnableds.
MultiLevelAnd(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class MultiLevelAnd: Creates using two MultiLevelOutputEnableds.
MultiLevelBinary - Class in org.anchoranalysis.io.output.enabled.multi
MultiLevelBinary(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class MultiLevelBinary
MultiLevelNot - Class in org.anchoranalysis.io.output.enabled.multi: The complement of an existing MultiLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
MultiLevelNot(MultiLevelOutputEnabled) - Constructor for class MultiLevelNot
MultiLevelOr - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in either of two MultiLevelOutputEnableds.
MultiLevelOr(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class MultiLevelOr: Creates using two MultiLevelOutputEnableds.
MultiLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.multi: Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
MultiLevelRecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Like RecordedOutputs but accepts two levels, first and second, like in a MultiLevelRecordedOutputs.
MultiLevelRecordedOutputs() - Constructor for class MultiLevelRecordedOutputs
MultiName - Interface in org.anchoranalysis.feature.io.name: A name that that uniquely identifies an entity, and is composed of two parts.
MultiNameFactory - Class in org.anchoranalysis.feature.io.name: Creates MultiName.
MultipleComparer - Class in org.anchoranalysis.annotation.io.bean.comparer: Allows comparison of an annotation with multiple other entities.
MultipleComparer() - Constructor for class MultipleComparer
MultipleFileTypeGenerator<T> - Interface in org.anchoranalysis.io.generator: A Generator that creates multiple different file-types.
multipleSeries() - Method in class PlotIndexBase
multiplex(boolean, boolean) - Static method in enum StackRGBState: Returns one of the three RGB_ states based upon two boolean flags.
multiplex(int, int, int) - Method in enum OutsideKernelPolicy: Multiplexes between three-values depending on which policy is currently selected.
multiplex(boolean) - Method in class RecordingWriters: Multiplexes between the selective and permissive writers based on a flag.
multiplexAlpha(boolean) - Static method in enum StackRGBState: Returns one of the two RGB_ states based upon a boolean flag.
multiplexPlural(long, String, String) - Static method in class LanguageUtilities: Returns a single or plural word depending on the number.
Multiply<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Multiply() - Constructor for class Multiply
multiplyBy(double) - Method in interface VoxelsArithmetic: Multiplies the value of all voxels by a factor.
multiplyBy(ObjectMask, double) - Method in interface VoxelsArithmetic: Multiplies each voxel by constant factor but only for voxels inside an ObjectMask.
MultiplyByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
MultiplyByConstant(Feature<T>, double) - Constructor for class MultiplyByConstant
MultiplyByConstant() - Constructor for class MultiplyByConstant
multiplyByConstant(double) - Method in class RotationMatrix: Multiplies each element in the rotation-matrix by a value.
MultiplyConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MultiplyConstant() - Constructor for class MultiplyConstant
MultiplyTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MultiplyTwoChannels(IntBinaryOperation) - Constructor for class MultiplyTwoChannels
MutableDirectory - Class in org.anchoranalysis.io.manifest.directory: An entry for a directory in the manifest, to which outputs and sub-directories can be later added.
MutableDirectory() - Constructor for class MutableDirectory
MutableDirectory(MutableDirectory) - Constructor for class MutableDirectory

N

name() - Method in class ClusterIdentifier: Derives a name for the cluster, based upon its contents.
NamedBean<T extends AnchorBean<?>> - Class in org.anchoranalysis.bean: A bean with an associated textual name.
NamedBean(String, T) - Constructor for class NamedBean
NamedBean() - Constructor for class NamedBean
NamedChannel - Class in org.anchoranalysis.plugin.image.task.grouped
NamedChannel(String, Channel) - Constructor for class NamedChannel
NamedChannels - Class in org.anchoranalysis.plugin.io.bean.input.channel: An image viewed as a set of channels, each with a unique name.
NamedChannels() - Constructor for class NamedChannels
NamedChannelsAppend - Class in org.anchoranalysis.plugin.io.bean.input.channel
NamedChannelsAppend() - Constructor for class NamedChannelsAppend
NamedChannelsBase - Class in org.anchoranalysis.plugin.io.bean.input.channel: Parent for all the NamedChannels classes
NamedChannelsBase() - Constructor for class NamedChannelsBase
NamedChannelsForSeries - Interface in org.anchoranalysis.image.io.channel.input.series
NamedChannelsForSeriesConcatenate - Class in org.anchoranalysis.image.io.channel.input.series
NamedChannelsForSeriesConcatenate() - Constructor for class NamedChannelsForSeriesConcatenate
NamedChannelsForSeriesMap - Class in org.anchoranalysis.image.io.channel.input.series
NamedChannelsForSeriesMap(OpenedImageFile, NamedEntries, int) - Constructor for class NamedChannelsForSeriesMap
NamedChannelsInput - Class in org.anchoranalysis.image.io.channel.input: Provides a set of channels as an input, with each channel having a name.
NamedChannelsInput() - Constructor for class NamedChannelsInput
NamedChannelsInputPart - Class in org.anchoranalysis.image.io.channel.input: One part of a NamedChannelsInput that can be combined with others.
NamedChannelsInputPart() - Constructor for class NamedChannelsInputPart
NamedChannelsQuick - Class in org.anchoranalysis.plugin.quick.bean.input: A particular type of NamedChannels which allows easier input of data, making several assumptions.
NamedChannelsQuick() - Constructor for class NamedChannelsQuick
NamedEntries - Class in org.anchoranalysis.image.io.channel.input: A map of image channel-names to indices (entries).
NamedEntries() - Constructor for class NamedEntries
NamedEntriesCreator - Class in org.anchoranalysis.image.io.channel.input
NamedEntriesCreator() - Constructor for class NamedEntriesCreator
NamedFeatureCalculateException - Exception in org.anchoranalysis.feature.calculate: An exception that occurs when a feature fails to successfully calculate.
NamedFeatureCalculateException(String) - Constructor for exception NamedFeatureCalculateException: Creates with a general failure message that doesn't pertain to any particular feature.
NamedFeatureCalculateException(Exception) - Constructor for exception NamedFeatureCalculateException: Creates with a calculation error that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String, String) - Constructor for exception NamedFeatureCalculateException: Creates with a failure message associated with a particular feature.
NamedFeatureCalculatorMulti<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.calculator: A FeatureCalculatorMulti with associated feature-names
NamedFeatureCalculatorMulti(FeatureCalculatorMulti<T>, FeatureNameList) - Constructor for class NamedFeatureCalculatorMulti
NamedFeatureStore<T extends FeatureInput> - Class in org.anchoranalysis.feature.store: Stores Features, each with an associated name, with list-like access and map-like access.
NamedFeatureStore() - Constructor for class NamedFeatureStore
NamedFeatureStoreFactory - Class in org.anchoranalysis.feature.store: Creates a NamedFeatureStore.
NamedFile - Class in org.anchoranalysis.io.input.file: A file with an associated unique name.
NamedFile(String, File) - Constructor for class NamedFile
NamedFiles - Class in org.anchoranalysis.plugin.io.bean.input.files: Implementation of NamedFilesBase that is an InputManager that accepts FileInput as input and derives a name.
NamedFiles(FilesProvider) - Constructor for class NamedFiles
NamedFiles(FilesProvider, FileNamer) - Constructor for class NamedFiles
NamedFiles() - Constructor for class NamedFiles
NamedFilesBase<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.files: Base class for an InputManager that produces inputs that are created from a NamedFile.
NamedFilesBase() - Constructor for class NamedFilesBase
NamedFilesBase(FileNamer) - Constructor for class NamedFilesBase
NamedFilesWithDirectory - Class in org.anchoranalysis.plugin.io.bean.input.files: Like NamedFiles but rather accepts a FileWithDirectoryInput rather than a FileInput.
NamedFilesWithDirectory() - Constructor for class NamedFilesWithDirectory
NamedPath - Class in org.anchoranalysis.io.output.path.prefixer: A path and associated name.
NamedPath(String, Path) - Constructor for class NamedPath
NamedProvider<T> - Interface in org.anchoranalysis.core.identifier.provider: A collection of elements, each with an associated name.
NamedProviderBridge<S,T> - Class in org.anchoranalysis.core.identifier.provider: Exposes elements in a NamedProvider as a different type.
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>) - Constructor for class NamedProviderBridge: Creates with a particular provider and bridge.
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>, boolean) - Constructor for class NamedProviderBridge
NamedProviderCombine<T> - Class in org.anchoranalysis.core.identifier.provider: Combines one more NamedProviders into a unitary NamedProvider.
NamedProviderCombine(Stream<NamedProvider<T>>) - Constructor for class NamedProviderCombine: Create from a stream of NamedProviders.
NamedProviderGetException - Exception in org.anchoranalysis.core.identifier.provider: When a get operation fails with a NamedProvider.
NamedProviderGetException(String, Throwable) - Constructor for exception NamedProviderGetException: Create with a particular cause.
NamedProviderOutputter<T> - Class in org.anchoranalysis.io.generator.collection: Outputs entities from a NamedProvider into a directory using the names of each entity for a corresponding generated file.
NamedProviderOutputter(NamedProvider<T>, Generator<T>, OutputterChecked) - Constructor for class NamedProviderOutputter
NamedProviderStore<T> - Interface in org.anchoranalysis.core.identifier.provider.store: A NamedProvider, in which items can also be added.
NamedStacks - Class in org.anchoranalysis.image.core.stack.named: A set of image-stacks each with a name.
NamedStacks() - Constructor for class NamedStacks
NamedStacksOutputter - Class in org.anchoranalysis.image.io.stack.output: Outputs a named-set of stacks, performing appropriate checks on what is enabled or not.
NamedStacksSupplier - Interface in org.anchoranalysis.image.core.stack.named: Supplies a NamedProvider of Stacks.
NamedStacksUniformSize - Class in org.anchoranalysis.image.core.stack.named: Like NamedStacks but enforces a condition that all stacks must have the same dimensions.
NamedStacksUniformSize() - Constructor for class NamedStacksUniformSize
nameFor(LocalDateTime, LocalDateTime, DateStyle, TimeStyle) - Method in class TimeIntervalNamer: Derives a name from the time-range in the cluster and some parameters.
NameValue<T> - Interface in org.anchoranalysis.core.identifier.name: A pair combining a name and a value.
NameValueMap<T> - Class in org.anchoranalysis.core.identifier.provider: Builds a mapping from names to values, given NameValue instances.
NameValueMap(Iterable<? extends NameValue<T>>) - Constructor for class NameValueMap: Creates and populates with elements from an Iterable.
NameValueMap() - Constructor for class NameValueMap
negative() - Method in class Orientation: Derives a new Orientation in the opposite (negative) direction to the current instance.
negative() - Method in class Orientation2D
negative() - Method in class Orientation3DEulerAngles
negative() - Method in class OrientationAxisAngle
negative() - Method in class OrientationRotationMatrix
NeighborGraph - Class in org.anchoranalysis.image.voxel.neighborhood: Creates a graph where each vertex represents an ObjectMask and edges between indicate that two objects neighbor each other.
Neighborhood - Interface in org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
NeighborhoodCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: A condition placed to determine if two objects could be potential neighbors are not (i.e.
NeighborhoodCondition(boolean, boolean) - Constructor for class NeighborhoodCondition
NeighborhoodFactory - Class in org.anchoranalysis.image.voxel.neighborhood: Creates either a big voxel-neighborhood or a small voxel-neighborhood.
NeighborPredicate - Interface in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: A predicate on whether a neighbor satisfies a condition in relation to a particular point that it neighbors.
newlinesBeforeError() - Method in class LauncherConfig: if true, then some extra newlines are inserted before error messages
newTemplateMark() - Method in class MarkWithIdentifierFactory
nextIndex(int) - Method in interface IndexRangeSeek: Finds the next index in the range after index.
nextValue() - Method in class PriorityQueueIndexRangeDownhill
NO_RESTRICTIONS - Static variable in class OutputSequenceStackFactory: A factory with no restrictions on what kind of stacks can be outputted.
NoAnnealing - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
NoAnnealing() - Constructor for class NoAnnealing
noInterpolation() - Method in class InterpolatorFactory: An Interpolator that is effectively disabled, and performs no interpolation, copying a single (minimal corner) value for each voxel.
None - Class in org.anchoranalysis.image.bean.interpolator
None() - Constructor for class None
None - Class in org.anchoranalysis.io.output.bean.enabled: No outputs are enabled.
None() - Constructor for class None
NoneExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are disabled except particular ones.
NoneExcept(StringSet) - Constructor for class NoneExcept: Create with first-level output names
NoneExcept() - Constructor for class NoneExcept
NonEmpty - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a collection must have at least one item.
nonExistingItem(String) - Static method in exception NamedProviderGetException: Creates using a standard-error message for a non-existing item
nonExistingItem(String, String) - Static method in exception NamedProviderGetException: Like NamedProviderGetException.nonExistingItem(String) but with a message that also includes a user-friendly-name for the NamedProvider.
NonImageFileFormat - Enum in org.anchoranalysis.core.format: Non image file-formats that are read or writeten to the filesystem, each with an associated extension.
NonNegative - Annotation Type in org.anchoranalysis.bean.annotation: The bean-field should have a value >= 0.
nonNegativeX() - Method in class KernelPointCursor: Whether the current point is non-negative in the X-dimension?
nonNegativeY() - Method in class KernelPointCursor: Whether the current point is non-negative in the Y-dimension?
noOverlapWith(Mark, int) - Method in interface QuickOverlapCalculation: A quick (computationally-efficient) test to see if we can reject the possibility of overlap
noPadding() - Method in class Padding
normalisedRadii(Ellipsoid, Optional<Resolution>) - Static method in class EllipsoidUtilities
normalize() - Method in class Tuple3d: Normalizes the tuple by dividing each component's value by the overall length.
NormalizeByConstant - Class in org.anchoranalysis.plugin.image.feature.bean.score
NormalizeByConstant() - Constructor for class NormalizeByConstant
NormalizeByMax - Class in org.anchoranalysis.plugin.image.feature.bean.score: This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
NormalizeByMax() - Constructor for class NormalizeByMax
NormalizeDifferenceToMedian - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Corrects a channel in the following way
NormalizeDifferenceToMedian() - Constructor for class NormalizeDifferenceToMedian
NormalizedPath - Class in org.anchoranalysis.plugin.io.bean.file.namer: Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
NormalizedPath() - Constructor for class NormalizedPath
NormalizedRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: The range of two feature values (i.e.
NormalizedRange() - Constructor for class NormalizedRange
NormalizeObjectIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
NormalizeObjectIntensity() - Constructor for class NormalizeObjectIntensity
noScaling(DisplayStack) - Static method in class ScaleableBackground: Creates a background from a stack without any scaling.
NoSharedState - Class in org.anchoranalysis.experiment.task: Fake shared-state to use to indicate none exists (for type safety)
Not - Class in org.anchoranalysis.plugin.mpp.bean.check
Not() - Constructor for class Not
NotFound<T> - Class in org.anchoranalysis.annotation.io.image.findable: A negative-result when an object is not found at a particular location.
NotFound(Path, String) - Constructor for class NotFound
Nothing - Class in org.anchoranalysis.image.io.bean.object.draw: Writes nothing for a particular object.
Nothing() - Constructor for class Nothing
notifyBuffer(LocalSlices, int) - Method in class AndKernel
notifyBuffer(LocalSlices, int) - Method in class ConditionalKernel
notifyBuffer(LocalSlices, int) - Method in class CountKernel
notifyBuffer(LocalSlices, int) - Method in class Kernel: Called to inform the Kernel of buffers that are currently being processed.
notifyBuffer(LocalSlices, int) - Method in class BinaryKernelMorphological
notifyBuffer(LocalSlices, int) - Method in class OutlineKernelNeighborMatchValue
notifyChangeSlice(int) - Method in interface PredicateBufferBinary: Notifies the processor that there has been a change in slice (z global coordinate).
notifyChangeSlice(int) - Method in interface PredicateKernelPointCursor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeSlice(int) - Method in interface ProcessBufferBinary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface ProcessBufferBinaryMixed: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface ProcessBufferBinaryWithoutOffset: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface ProcessBufferTernary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface ProcessBufferUnary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface ProcessKernelPointCursor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeSlice(int) - Method in interface ProcessPoint: Notifies the processor that there has been a change in Z-coordinate.
notifyChangeSlice(int) - Method in interface ProcessPointAndIndex: Notifies the processor that there has been a change in Z-coordinate.
notifyChangeY(int) - Method in interface ProcessPoint: Notifies the processor that there has been a change in Y-coordinate.
notifyChangeY(int) - Method in interface ProcessPointAndIndex: Notifies the processor that there has been a change in Y-coordinate.
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in interface ProcessChangedPointAbsoluteMasked: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int) - Method in interface ProcessVoxelNeighbor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int, int) - Method in interface ProcessVoxelNeighborAbsolute: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
NoTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Base class for ImageJRasterWriter that doesn't support writing time-series as a stack.
NoTimeSeries() - Constructor for class NoTimeSeries
NotInContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters objects to keep only those which are NOT in the container.
NotInContainer() - Constructor for class NotInContainer
NotTouchingSceneBorder - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps only objects that are not adjacent to the scene-border (i.e.
NotTouchingSceneBorder() - Constructor for class NotTouchingSceneBorder
NullInitialization - Class in org.anchoranalysis.bean.initializable.parameters: When initialization should occur of a bean, but no parameters (containing data) are required.
NullMessageLogger - Class in org.anchoranalysis.core.log: Does nothing with with any messages logged.
NullMessageLogger() - Constructor for class NullMessageLogger
NullParametersBean<T> - Class in org.anchoranalysis.bean: A base class for beans that require initialization but the initializations needs no parameters.
NullParametersBean() - Constructor for class NullParametersBean: Default constructor.
NullReporter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Dummy reporter that takes no action.
NullReporter() - Constructor for class NullReporter
NUM_OBJECTS_ATTRIBUTE_NAME - Static variable in class HDF5ObjectsGenerator
NUMBER_DECIMAL_PLACES - Static variable in class FeatureCSVWriter: The number of decimal places to use for double values, unless visuallyShortened==true.
NUMBER_DIGITS_IN_OUTPUT - Static variable in class PeriodicSubdirectoryReporter
NUMBER_ELEMENTS_WRITTEN_ERRORED - Static variable in class WriterRouterErrors
NUMBER_ELEMENTS_WRITTEN_NOT_ALLOWED - Static variable in class CheckIfAllowed
numberBorderPixels(ObjectMask, KernelApplicationParameters) - Static method in class NumberVoxelsAtBorder
numberBytes() - Method in class VoxelDataType: The number of bytes needed to represent this data-type.
numberChannels(Logger) - Method in class NamedChannelsInput: Number of channels.
numberChannels() - Method in interface NamedChannelsForSeries: The number of channels that exist for the series.
numberChannels() - Method in class NamedChannelsForSeriesConcatenate
numberChannels() - Method in class NamedChannelsForSeriesMap
numberChannels(Logger) - Method in interface OpenedImageFile: The number of channels in the image-file e.g.
NumberChannels - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of channels in an image.
NumberChannels() - Constructor for class NumberChannels
NumberChannels - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The number of channels in an image-stack.
NumberChannels() - Constructor for class NumberChannels
NumberChannels - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
NumberChannels() - Constructor for class NumberChannels
numberChannels(Logger) - Method in class OpenedMultiFile
numberCompletedFailed() - Method in class TaskStatistics: The number of jobs that completed with failure.
numberCompletedFailureJobs() - Method in class ConcurrentJobMonitor
numberCompletedJobs() - Method in class ConcurrentJobMonitor
numberCompletedSuccess() - Method in class TaskStatistics: The number of jobs that completed successfully.
numberCompletedSuccessfullyJobs() - Method in class ConcurrentJobMonitor
numberCompletedTotal() - Method in class TaskStatistics: The number of jobs that completed in total.
numberDimensions() - Method in class Circle
numberDimensions() - Method in class Ellipse
numberDimensions() - Method in class Ellipsoid
numberDimensions() - Method in class Sphere
numberDimensions() - Method in class Mark
numberDimensions() - Method in class LineSegment
numberDimensions() - Method in class PointList
numberDimensions() - Method in class Polygon
numberDimensions() - Method in class PolygonCurve
numberDimensions() - Method in class RotatableBoundingBox
numberDimensions() - Method in class Orientation: The dimensionality of space the orientation is valid for.
numberDimensions() - Method in class Orientation2D
numberDimensions() - Method in class Orientation3DEulerAngles
numberDimensions() - Method in class OrientationAxisAngle
numberDimensions() - Method in class OrientationRotationMatrix
numberDisabled() - Method in class RecordedOutputs: Number of output-names that were not enabled.
numberDistinctChannelsSource() - Method in class ImageFileEncoding: When RGB-encoded and non-interleaved, the source array is considered 1 channel (not three).
NumberDistinctValues - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Number of unique values in histogram.
NumberDistinctValues() - Constructor for class NumberDistinctValues
numberEdges() - Method in class GraphWithoutPayload: The number of edges in the graph.
numberEdges() - Method in class GraphWithPayload: The number of edges in the graph.
numberEnabled() - Method in class RecordedOutputs: Number of output-names that were enabled.
numberExecutingJobs() - Method in class ConcurrentJobMonitor
numberFrames() - Method in class NamedChannelsInput
numberFrames(Logger) - Method in interface OpenedImageFile: The number of frames in the image-file i.e.
numberFrames() - Method in interface ProvidesStackInput
numberFrames() - Method in class MultiInput
NumberFrames - Class in org.anchoranalysis.plugin.image.feature.bean.metadata: The number of frames in an image.
NumberFrames() - Constructor for class NumberFrames
numberFrames() - Method in class ConvertNamedChannelsInputToStack
numberFrames(Logger) - Method in class OpenedMultiFile
numberGroups() - Method in class GroupedAnnotationLabels
numberImageFeatures() - Method in class MergedPairsFeatures
NumberIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
NumberIntersectingObjects() - Constructor for class NumberIntersectingObjects
NumberIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
NumberIntersectingObjectsAboveThreshold() - Constructor for class NumberIntersectingObjectsAboveThreshold
numberItemsCurrentlyStored() - Method in class CalculationPartMap: Number of items currently stored in cache.
NumberIterations - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination: Terminates after a specific number of iterations.
NumberIterations(int) - Constructor for class NumberIterations
NumberIterations() - Constructor for class NumberIterations
NumberIterationsBase - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination: Parent class for a TerminationCondition where the number-of-iterations is a bean-field.
NumberIterationsBase() - Constructor for class NumberIterationsBase
NumberIterationsBase(int) - Constructor for class NumberIterationsBase
numberManifests() - Method in class ManifestCouplingDefinition
NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
NumberMarks() - Constructor for class NumberMarks
NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
NumberMarks() - Constructor for class NumberMarks
NumberMarksFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
NumberMarksFromManifest() - Constructor for class NumberMarksFromManifest
numberMatches() - Method in class MatchedObject: The number of objects in matches.
NumberNeighboringVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Calculates the number of voxels on the object that have a neighbor.
NumberNeighboringVoxels() - Constructor for class NumberNeighboringVoxels
numberNotCompleted() - Method in class TaskStatistics: Number of jobs that have not been completed.
NumberObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.collection
NumberObjects() - Constructor for class NumberObjects
numberOngoingJobs() - Method in class ConcurrentJobMonitor
numberPaired() - Method in interface Assignment: The number of items that are paired.
numberPaired() - Method in class ObjectVoxelIntersection
numberPaired() - Method in class OverlappingObjects
numberPairFeatures() - Method in class MergedPairsFeatures
NumberPoints - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
NumberPoints() - Constructor for class NumberPoints
numberRegions() - Method in class Ellipse
numberRegions() - Method in class Ellipsoid
numberRegions() - Method in class MarkWithPositionAndSingleRadius
numberRegions() - Method in class Mark
numberRegions() - Method in class LineSegment
numberRegions() - Method in class PointList
numberRegions() - Method in class Polygon
numberRegions() - Method in class PolygonCurve
numberRegions() - Method in class RotatableBoundingBox
NumberRemovedVoxelsAfterClosing - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: How many pixels are removed after a morphological closing operation on the object-mask.
NumberRemovedVoxelsAfterClosing() - Constructor for class NumberRemovedVoxelsAfterClosing
numberSeries() - Method in class NamedChannelsInput: Number of series that exist.
numberSeries() - Method in interface OpenedImageFile: The number of series (distinct sets of images) in the image-file.
numberSeries() - Method in class OpenedMultiFile
numberSingleFeatures() - Method in class MergedPairsFeatures
numberSlices() - Method in interface VoxelPartition
numberSlices() - Method in class VoxelPartitionHistogram
NumberToStringConverter - Class in org.anchoranalysis.plugin.io.shared: Converts a number to a strings of constant width by padding with leading zeros.
NumberToStringConverter(int) - Constructor for class NumberToStringConverter: Creates with a constant width just enough to be able to represent maxNumberToRepresent.
numberTotalScheduledJobs() - Method in class TaskStatistics: Total number of scheduled jobs.
NumberTouchingVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting the touching voxels by intersection of object-masks
NumberTouchingVoxelFaces() - Constructor for class NumberTouchingVoxelFaces
NumberTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting touching voxels.
NumberTouchingVoxels() - Constructor for class NumberTouchingVoxels
numberUnassigned(boolean) - Method in interface Assignment: The number of items in a particular set that are not paired.
numberUnassigned(boolean) - Method in class ObjectVoxelIntersection
numberUnassigned(boolean) - Method in class OverlappingObjects
numberUnassignedLeft() - Method in class OverlappingObjects: The number of unassigned objects in the left set.
numberUnassignedRight() - Method in class OverlappingObjects: The number of unassigned objects in the right set.
numberUniqueColors() - Method in interface ColorIndex: The number of unique colors being described by the index.
numberUniqueColors() - Method in class ColorIndexModulo
numberUniqueColors() - Method in class ColorList
numberUniqueColors() - Method in class SingleColor
numberVertices() - Method in class GraphWithoutPayload: The number of vertices in the graph.
numberVertices() - Method in class GraphWithPayload: The number of vertices in the graph.
NumberVoxels - Class in org.anchoranalysis.image.feature.bean.object.single
NumberVoxels() - Constructor for class NumberVoxels
numberVoxels() - Method in class ObjectVertex
NumberVoxelsAtBorder - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
NumberVoxelsAtBorder() - Constructor for class NumberVoxelsAtBorder
numberVoxelsOn() - Method in class ObjectMask: The number of on voxels on the object-mask.
numFrames() - Method in class StackWithMap
numRegions() - Method in class RegionMap
numSlices() - Method in class IndexByRegion
numSlices() - Method in class SortedSetChannel

O

ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
ObjectAggregationBase() - Constructor for class ObjectAggregationBase
ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Writes an object-mask as a mask (i.e.
ObjectAsMaskGenerator() - Constructor for class ObjectAsMaskGenerator: Creates using a default image-resolution.
ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class ObjectAsMaskGenerator
ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
ObjectAsPoints() - Constructor for class ObjectAsPoints
ObjectCollection - Class in org.anchoranalysis.image.voxel.object: A collection of ObjectMasks.
ObjectCollection() - Constructor for class ObjectCollection: Creates with no objects.
ObjectCollection(Stream<ObjectMask>) - Constructor for class ObjectCollection: Creates with elements from a stream.
ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object: Creates ObjectCollection using various utility and helper methods.
ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide an ObjectCollection.
ObjectCollectionProvider() - Constructor for class ObjectCollectionProvider
ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
ObjectCollectionProviderFilterBase() - Constructor for class ObjectCollectionProviderFilterBase
ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
ObjectCollectionProviderMorphological() - Constructor for class ObjectCollectionProviderMorphological
ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider: Base class for ObjectCollectionProvider that take a objects bean-field of same type as provided.
ObjectCollectionProviderUnary() - Constructor for class ObjectCollectionProviderUnary
ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
ObjectCollectionProviderWithFeature() - Constructor for class ObjectCollectionProviderWithFeature
ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input: Reads an ObjectCollection from the filesystem
ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties: Like an ObjectCollection but each object has associated properties.
ObjectCollectionWithProperties() - Constructor for class ObjectCollectionWithProperties: Create with zero objects.
ObjectCollectionWithProperties(ObjectMask) - Constructor for class ObjectCollectionWithProperties: Create with a single object.
ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class ObjectCollectionWithProperties: Create with a stream of objects with properties.
ObjectCollectionWithProperties(ObjectCollection) - Constructor for class ObjectCollectionWithProperties: Create with a stream of objects, assign empty properties to each.
ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties: Creates ObjectCollectionWithProperties.
ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter: Copies an area corresponding to an object-mask to another Voxels.
ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer: A means of extracting attributes associated with a particular object (e.g.
ObjectDrawAttributes(ColorIndex) - Constructor for class ObjectDrawAttributes: Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class ObjectDrawAttributes
ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
ObjectFilter - Class in org.anchoranalysis.image.bean.object: Base class for filtering an ObjectCollection to remove objects according to a criteria.
ObjectFilter() - Constructor for class ObjectFilter
ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: A filter that combines other filters (in a list)
ObjectFilterCombine() - Constructor for class ObjectFilterCombine
ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter: Uses a predicate to make a decision whether to keep objects or not.
ObjectFilterPredicate() - Constructor for class ObjectFilterPredicate
ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter: An independent object-filter that uses a relation in its predicate.
ObjectFilterRelation() - Constructor for class ObjectFilterRelation
objectFor(T) - Method in interface AccessObjectMask: An object-mask for a given element.
objectFor(ObjectMask) - Method in class AccessObjectMaskSimple
ObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object: Create an ObjectMask from a collection of points.
ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes using Java's Native serialization framework.
ObjectInputStreamDeserializer() - Constructor for class ObjectInputStreamDeserializer
ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
ObjectMask - Class in org.anchoranalysis.image.voxel.object: A localized-mask in an image, expressed as a BoundingBox, with a corresponding mask sized to match the bounding-box.
ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates from a Voxels mask that is cornered at the origin.
ObjectMask(BoundingBox) - Constructor for class ObjectMask: Creates as a bounding-box with all corresponding mask voxels set to off.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates from a BoundedVoxels with UnsignedByteBuffer.
ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates from a BinaryVoxels to be located at the origin.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates from Voxels and a BoundingBox with default BinaryValuesInt.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class ObjectMask: Creates from Voxels and a corresponding BoundingBox and BinaryValuesInt.
ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates from a BinaryVoxels and a corresponding bounding-box.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class ObjectMask: Creates from BoundedVoxels and corresponding BinaryValuesInt.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class ObjectMask: Like ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the binary-values as bytes.
ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge: Merges one or more ObjectMasks into a single object.
ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object: A custom "stream" like class for various functional-programming operations on ObjectCollection
ObjectMaskStream(ObjectCollection) - Constructor for class ObjectMaskStream
ObjectMatcher - Class in org.anchoranalysis.image.bean.object: Matches an object with other objects.
ObjectMatcher() - Constructor for class ObjectMatcher
ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
ObjectOutputStreamGenerator() - Constructor for class ObjectOutputStreamGenerator
ObjectOutputStreamGenerator(Optional<String>) - Constructor for class ObjectOutputStreamGenerator
ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
ObjectRadiusStandardDeviation() - Constructor for class ObjectRadiusStandardDeviation
objects() - Method in class ImageInitialization
objects() - Method in class MultiInput
OBJECTS - Static variable in class OutputterDirectories: Where collections of objects are typically placed in a define-experiment output
Objects - Class in org.anchoranalysis.plugin.annotation.bean.comparer: An ObjectCollection to be compared against something else.
Objects() - Constructor for class Objects
objects(String) - Static method in class ReferenceFactory
OBJECTS_ROOT - Static variable in class HDF5PathHelper: Hardcoded string that identifies in the HDF5 file for where the object-collection is stored
OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class HDF5PathHelper: Adds seperators before and after the OBJECTS_ROOT_PATH
ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Base class for generators that accept a set of objects as input.
ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class ObjectsAsGrayscaleGenerator
ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: A base class for generators that draw objects on top of a RGB-Stack.
ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class ObjectsAsRGBGenerator
ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects as a Raster with unique id values for each object.
ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class ObjectsAsUniqueValueGenerator
ObjectScalingMethod - Interface in org.anchoranalysis.image.core.object.scale.method: A way to scale a group of ObjectMasks, scaling each object independently or collectively.
ObjectScalingMethodFactory - Class in org.anchoranalysis.image.core.object.scale.method: Determines which instance of ObjectScalingMethod to apply.
ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ObjectSerializerPeriodicReporter(String) - Constructor for class ObjectSerializerPeriodicReporter
objectsForThumbnail(T) - Method in class CombineObjectsForFeatures: Selects objects from an input that will be used for thumbnail generation
objectsForThumbnail(FeatureInputSingleObject) - Method in class EachObjectIndependently
objectsForThumbnail(FeatureInputPairObjects) - Method in class PairNeighbors
ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected: Creates a ObjectCollection from the connected-components of a mask or binary-voxels.
ObjectsFromConnectedComponentsFactory() - Constructor for class ObjectsFromConnectedComponentsFactory: Creates to use a small-neighborhood.
ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class ObjectsFromConnectedComponentsFactory: Creates to use a specified type of neighborhood.
ObjectsFromConnectedComponentsFactory(int) - Constructor for class ObjectsFromConnectedComponentsFactory: Creates to use a minimum number of voxels for each connected component.
ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class ObjectsFromConnectedComponentsFactory: Creates to use a specified type of neighborhood, and minimum number of voxels.
objectsFromOverlays(OverlayCollection) - Static method in class OverlayCollectionObjectFactory: Creates objects from whatever Overlays are found in the collection *
ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects merged together as a mask.
ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class ObjectsMergedAsMaskGenerator
ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class ObjectsToCompare
objectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator: The objects to draw (without any colors) on the background
objectsToDraw(Dimensions) - Method in class ColoredObjects
objectsToDraw(Dimensions) - Method in class ColoredMarks
ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge: A vertex in a merge graph representing an object (and and an associated payload)
ObjectVertex(ObjectMask, double) - Constructor for class ObjectVertex
ObjectVoxelIntersection - Class in org.anchoranalysis.annotation.io.assignment: Creates an assignment between intersecting voxels in two objects.
ObjectVoxelIntersection(ObjectMask, ObjectMask) - Constructor for class ObjectVoxelIntersection: Determines a voxel-assignment between two objects.
ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Like ObjectAsMaskGenerator but additionally outputs a serialized bounding box.
ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class ObjectWithBoundingBoxGenerator
ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class ObjectWithEllipse
ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature-value from a collection.
ObjectWithMaximumFeature() - Constructor for class ObjectWithMaximumFeature
ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature among a group of matches for each object.
ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class ObjectWithMaximumFeatureFromEachMatchedCollection
ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties: An ObjectMask with associated key-value properties.
ObjectWithProperties(BoundingBox) - Constructor for class ObjectWithProperties: Creates as a bounding-box with all corresponding mask voxels set to off.
ObjectWithProperties(ObjectMask) - Constructor for class ObjectWithProperties: Creates with an existing ObjectMask and empty properties.
ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class ObjectWithProperties
obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class AggregateTriggerBank
obtain(int, PeriodReceiver<S>) - Method in class PeriodTriggerBank
of(Stream<T>) - Static method in class FunctionalList: Creates a list from a stream.
of(boolean) - Static method in class ObjectScalingMethodFactory: Determines which method to use, given circumstances.
of(boolean, boolean) - Static method in enum OutsideKernelPolicy: Multiplexes between all three possible enums.
of(boolean) - Static method in class NeighborhoodFactory: Gets an appropriate neighborhood
of(ObjectMask...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements from the parameter-list.
of(ObjectCollection...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements copied from existing collections.
of(Optional<ObjectCollection>...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements copied from existing collections, if they exist.
of(Collection<ObjectMask>...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements copied from existing collections.
of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entirety to an object-mask at the origin.
of(CalculationPartResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class CalculateShellObjectMask
of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateDilation
of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
of(FeatureCalculationInput<FeatureInputSingleObject>, boolean) - Static method in class CalculateEllipsoidLeastSquares
offset(int, int) - Method in class Dimensions: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offset(Point3i) - Method in class Dimensions: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
offset(int, int) - Method in class Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offset(int, int, int) - Method in class Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
offset(ReadableTuple3i) - Method in class Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
offset(Point2i) - Method in class Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offsetGlobal(int, int) - Method in class ObjectMask: Calculates an offset for locating a voxel inside the buffer, with global encoding of coordinates.
offsetRelative(int, int) - Method in class ObjectMask: Calculates an offset for locating a voxel inside the buffer, with local encoding of coordinates.
offsetSlice(Point3i) - Method in class Dimensions: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
offsetSlice(ReadableTuple3i) - Method in class Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a PointTwoDimensionalConsumer but also has a buffer offset.
OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer: Like a ScalarTwoDimensionalConsumer but accepts two coordinates of a point and an offset value.
ofResolved(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
OMETiff - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as an OME-TIFF using the Bioformats library.
OMETiff() - Constructor for class OMETiff: Default constructor.
OMEXML - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as an OME-XML using the Bioformats library.
OMEXML() - Constructor for class OMEXML: Default constructor.
One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects one specific channel from a set of stacks
One() - Constructor for class One
oneOnly(String, String, boolean, boolean) - Static method in class CheckMisconfigured: Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer: A base-class for a raster-writer that writes only one or three channeled images, and a flexible extension.
OneOrThreeChannelsWriter() - Constructor for class OneOrThreeChannelsWriter
OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
OneStageGenerator() - Constructor for class OneStageGenerator
ongoingTasksLessThan(int) - Method in class ConcurrentJobMonitor
onInitialization(P) - Method in class InitializableBean: Called after initialization.
onInitialization(NullInitialization) - Method in class NullParametersBean
onInitialization() - Method in class NullParametersBean: As there's no parameters we expose a different method.
onInitialization(DictionaryInitialization) - Method in class DictionaryProviderReference
onInitialization(FeatureInitialization) - Method in class Feature: Called after initialization.
onInitialization(FeatureRelatedInitialization) - Method in class ReferencingFeatureListProvider
onInitialization(ImageInitialization) - Method in class BinarySegmentationReference
onInitialization() - Method in class MarkWithIdentifierFactory
onInitialization(ImageInitialization) - Method in class FromInput
onInitialization(ImageInitialization) - Method in class FromChannel
onInitialization(ImageInitialization) - Method in class Reference
onInitialization(ImageInitialization) - Method in class FromStackChannel
onInitialization(ImageInitialization) - Method in class ReferenceOrElse
onInitialization(ImageInitialization) - Method in class FromInput
onInitialization(FeatureRelatedInitialization) - Method in class PermuteFeature
onInitialization(MarksInitialization) - Method in class FeatureValueCheckMark
onInitialization(MarksInitialization) - Method in class MarkProposerReference
onInitialization(MarksInitialization) - Method in class MarkMergeProposerReference
onInitialization(MarksInitialization) - Method in class MarkSplitProposerReference
onInitialization(MarksInitialization) - Method in class KernelMerge
onInitialization(PointsInitialization) - Method in class Reference
OnlyIf - Class in org.anchoranalysis.experiment.bean.log: Logs messages to a particular location ONLY if certain conditions are fulfilled.
OnlyIf() - Constructor for class OnlyIf
OnnxModel - Class in org.anchoranalysis.plugin.onnx.model: A model that can be used for inference using the ONNX Runtime's Java API.
OnnxModel(OrtSession) - Constructor for class OnnxModel
open() - Method in interface Progress: Begins tracking progress, to be called before any calls to Progress.update(int).
open() - Method in class ProgressConsole
open() - Method in class ProgressIgnore
open() - Method in class ProgressIncrement: Begins tracking progress, to be called before any calls to ProgressIncrement.update().
open(Logger) - Method in interface OpenedImageFile: Open the first series when we don't have a specific-type.
open(int, Logger) - Method in interface OpenedImageFile: Open when we don't have a specific-type.
open(int, Progress, Logger) - Method in interface OpenedImageFile: Like OpenedImageFile.open(int, Logger) but additionally tracks progress of the opening.
open(Path) - Static method in class CSVReaderByLine: Default reader, using comma and first-line headers
open(Path, String, boolean) - Static method in class CSVReaderByLine: Default reader, using comma and first-line headers
open(Path, String, boolean, boolean) - Static method in class CSVReaderByLine: Default reader, using comma and first-line headers
open(int, Progress, Logger) - Method in class OpenedMultiFile
openCheckType(int, Progress, VoxelDataType, Logger) - Method in interface OpenedImageFile: Opens a time-series, and checks that it is a particular type.
OpenCVModel - Class in org.anchoranalysis.plugin.opencv.segment: A model that can be used for inference using OpenCV's DNN module.
OpenCVModel(Net) - Constructor for class OpenCVModel
OpenCVReader - Class in org.anchoranalysis.plugin.opencv.bean.stack: Reads a stack from the file-system using OpenCV.
OpenCVReader() - Constructor for class OpenCVReader
OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.stack: Writes a stack to the file-system using OpenCV and a specified extension.
OpenCVWriter() - Constructor for class OpenCVWriter
OpenedCSVFile() - Constructor for class CSVReader.OpenedCSVFile
OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input: An image file that has been opened for reading containing one or more series of image-Stacks.
OpenedMultiFile - Class in org.anchoranalysis.plugin.io.multifile: A OpenedImageFile where the image is formed from more than one file on the file-system.
OpenedMultiFile(StackReader, ParsedFilePathBag) - Constructor for class OpenedMultiFile
openFile(Path, StackReader, Logger) - Method in class ImageMetadataReader: Opens a file containing one or more images but does not read an image.
openFile(Path) - Method in class StackReader: Opens a file containing one or more images.
openFile(Path, CalculateOrientationChange) - Method in class StackReaderOrientationCorrection: Opens a file containing one or more images but does not read an image.
openFile(Path) - Method in class BioformatsReader
openFile(Path, CalculateOrientationChange) - Method in class BioformatsReader
openFile(Path, StackReader, Logger) - Method in class AlwaysReject
openFile(Path, StackReader, Logger) - Method in class FromStackReader
openFile(Path, StackReader, Logger) - Method in class InferFromHeader
openFile(Path) - Method in class BranchExtension
openFile(Path) - Method in class FlattenAsChannel
openFile(Path) - Method in class ImposeResolution
openFile(Path) - Method in class MultiFileReader
openFile(Path) - Method in class ReadVoxelExtentXml
openFile(Path) - Method in class RejectIfConditionXYResolution
openFile(Path) - Method in class RotateImageToMatchEXIFOrientation
openFile(Path, CalculateOrientationChange) - Method in class RotateImageToMatchEXIFOrientation
openFile(Path) - Method in class OpenCVReader
openMarksFromFilePath(Path) - Static method in class TestLoaderMarks
openMarksFromTestPath(String) - Method in class TestLoaderMarks
openMask(StackReader, Path, BinaryValuesInt, Logger) - Static method in class MaskReader: Utility functions for opening a single-channeled stack as a Mask.
openXmlAbsoluteFilePath(String) - Static method in class TestLoader: Opens a XML document - with an absolute path on the filesystem.
openXmlAbsoluteFilePath(Path) - Static method in class TestLoader: Opens a XML document - with an absolute path on the filesystem.
openXmlFromTestPath(String) - Method in class TestLoader: Opens a XML document - with a path relative to the test root.
OperationFailedException - Exception in org.anchoranalysis.core.exception: Generic checked exception that can be thrown when a particular operation fails.
OperationFailedException(String) - Constructor for exception OperationFailedException: Creates with only a message.
OperationFailedException(Throwable) - Constructor for exception OperationFailedException: Creates with only a cause.
OperationFailedException(String, Throwable) - Constructor for exception OperationFailedException: Creates with both a message and cause.
OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception: Generic runtime exception that can be thrown when a particular operation fails.
OperationFailedRuntimeException(String) - Constructor for exception OperationFailedRuntimeException: Creates with only a message.
OperationFailedRuntimeException(Exception) - Constructor for exception OperationFailedRuntimeException: Creates with only a cause.
OperationMap<T> - Class in org.anchoranalysis.mpp.io.input: Stores objects as operations
OperationMap() - Constructor for class OperationMap
OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class OptimizationContext
OptimizationScheme<S,U,V> - Class in org.anchoranalysis.mpp.segment.bean.optimization: An optimization-scheme that uses kernels to make changes to state.
OptimizationScheme() - Constructor for class OptimizationScheme
OptimizationStep<S,T,V> - Class in org.anchoranalysis.mpp.segment.optimization.step
OptimizationStep() - Constructor for class OptimizationStep
OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
OptimizationStepLogReporter() - Constructor for class OptimizationStepLogReporter
OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception OptimizationTerminatedEarlyException
OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must always have a non-null value.
OptionalFactory - Class in org.anchoranalysis.core.functional: Utility functions to create Optional from flags.
OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined: A simple container expressing a value and an associationed optional name.
OptionalNameValue(Optional<String>, V) - Constructor for class OptionalNameValue
OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
OptionalProviderFactory - Class in org.anchoranalysis.bean: Utility functions to create Optional from nullable Providers.
OptionalUtilities - Class in org.anchoranalysis.core.functional: Additional utility functions for Optional and exceptions.
or(StackWriteAttributes) - Method in class StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical or on each field.
Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
Or() - Constructor for class Or
Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical OR i.e.
Or() - Constructor for class Or
order(String) - Method in interface OrderProvider
OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
OrderedList() - Constructor for class OrderedList
orderedListOfFeatures() - Method in class AddCriteriaEnergyPair
orderedListOfFeatures() - Method in class AddCriteriaNever
orderedListOfFeatures() - Method in class AddCriteriaOr
orderedListOfFeatures() - Method in class ArbitraryPointCommon
orderedListOfFeatures() - Method in class BoundingBoxIntersection
orderedListOfFeatures() - Method in interface OrderedFeatureList: A list of features used to determine the AddCriteria, or Optional.empty() if irrelvant.
orderedListOfFeatures() - Method in class AddCriteriaFeatureRelationThreshold
OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
OrderedRadius() - Constructor for class OrderedRadius
OrderProvider - Interface in org.anchoranalysis.io.manifest.sequencetype
orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class OptionalUtilities: Like Optional.orElseGet(java.util.function.Supplier<? extends T>) but tolerates an exception in the supplier function, which is immediately thrown.
orElseGetFlat(Optional<T>, CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities: Like OptionalUtilities.orElseGet(java.util.Optional<T>, org.anchoranalysis.core.functional.checked.CheckedSupplier<T, E>) but returns a Optional and can chain many alternatives.
orFlat(Iterable<Optional<T>>) - Static method in class OptionalUtilities: The first optional if it's present, or the second, or the third etc.
orFlat(Stream<Optional<T>>) - Static method in class OptionalUtilities: The first optional if it's present, or the second, or the third etc.
orFlat(Optional<T>...) - Static method in class OptionalUtilities: Like OptionalUtilities.orFlat(Iterable) but allows Optionals to be specified as variable-arguments.
orFlatSupplier(Iterable<CheckedSupplier<Optional<T>, E>>) - Static method in class OptionalUtilities: The first optional if it's present, or the second, or the third etc.
orFlatSupplier(CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities: Like OptionalUtilities.orFlatSupplier(Iterable) but allows Optionals to be specified as variable-arguments.
org.anchoranalysis.annotation - package org.anchoranalysis.annotation: Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image: Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io: Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment: A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator: Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean: Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer: What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.comparer - package org.anchoranalysis.annotation.io.comparer: Non-bean classes involving comparing results and annotations.
org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image: Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable: The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark: Reading and writing Mark-related annotations from/to the file-system.
org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark: Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean - package org.anchoranalysis.bean: Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation: Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define: Define and related-classes.
org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder: DefineAdder and related-classes.
org.anchoranalysis.bean.exception - package org.anchoranalysis.bean.exception: Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable: Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.parameters - package org.anchoranalysis.bean.initializable.parameters: Some parameterization used when initializing beans.
org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property: Initializating a bean with parameters.
org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute: Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.assign - package org.anchoranalysis.bean.permute.assign: Imposes a permutation value on one or more properties of a bean.
org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property: Applying permutations to the properties of a bean.
org.anchoranalysis.bean.primitive - package org.anchoranalysis.bean.primitive: Beans that implement collections of primitive element types, as well as String.
org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared: Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color: Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme: Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.dictionary - package org.anchoranalysis.bean.shared.dictionary: Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path: Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random: Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex: Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation: Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold: Specifies a unary relation to a threshold value.
org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml: Reading Beans from XML files.
org.anchoranalysis.bean.xml.creator - package org.anchoranalysis.bean.xml.creator: Creates beans from XML.
org.anchoranalysis.bean.xml.exception - package org.anchoranalysis.bean.xml.exception: Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory: Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.bean.xml.factory.primitive - package org.anchoranalysis.bean.xml.factory.primitive: Factories to create beans in org.anchoranalysis.bean.primitive.
org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher: Launching the anchor GUI interactive application from command-line.
org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache: Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.color - package org.anchoranalysis.core.color: Specifying particular colors and groups of colors.
org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception: Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable: Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly: Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.format - package org.anchoranalysis.core.format: File formats and associated extensions.
org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional: Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked: Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.functional.unchecked - package org.anchoranalysis.core.functional.unchecked: Adds additional functional-interfaces, that are unavailable in java.util.function, and do not throw checked exceptions.
org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph: Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter: Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name: Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider: A collection of named-elements, a NamedProvider and related operations.
org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store: Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index - package org.anchoranalysis.core.index: Classes to support getting / setting / specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.range - package org.anchoranalysis.core.index.range: A range of indices from minimum to maximum.
org.anchoranalysis.core.log - package org.anchoranalysis.core.log: Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error: Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress: Classes to allow for tracking the progress of a task that can be broken into smaller units, for reporting to the user.
org.anchoranalysis.core.random - package org.anchoranalysis.core.random: Generating random numbers.
org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize: Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system - package org.anchoranalysis.core.system: Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path: Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.time - package org.anchoranalysis.core.time: Recording the execution-time of operations for profiling.
org.anchoranalysis.core.value - package org.anchoranalysis.core.value: Encapsulating values or sets of named-values.
org.anchoranalysis.experiment - package org.anchoranalysis.experiment: Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.arguments - package org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment in addition to its bean specification.
org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean: Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier: Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io: Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log: Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor: How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require: A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task: Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io: Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log: Helpful classes for logging.
org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task: Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor: Non-bean classes related to JobProcessor.
org.anchoranalysis.experiment.time - package org.anchoranalysis.experiment.time: How long particular operations take to execute.
org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean: Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list: A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator: Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider: Provider of a single feature.
org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results: Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate: Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.bound - package org.anchoranalysis.feature.calculate.bound: Interfaces like FeatureCalculator but bound to particular features.
org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache: Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.calculate.cache.part - package org.anchoranalysis.feature.calculate.cache.part: Equivalent classes to org.anchoranalysis.feature.calculate.part after having been resolved against a cache.
org.anchoranalysis.feature.calculate.part - package org.anchoranalysis.feature.calculate.part
org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy: A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.initialization - package org.anchoranalysis.feature.initialization: Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input: Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv: Writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name: Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results: Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.calculation - package org.anchoranalysis.feature.io.results.calculation
org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group: Various different outputs that can be written for the a grouped version of the results in FeatureCalculationResults.
org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name: Data objects for the names of features.
org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results: Results from one or more feature calculations.
org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session: A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache: Creates a FeatureCalculationCache to use during feature-calculations.
org.anchoranalysis.feature.session.cache.finder - package org.anchoranalysis.feature.session.cache.finder: Strategies to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator: Base classes for methods to calculate results from features.
org.anchoranalysis.feature.session.replace - package org.anchoranalysis.feature.session.replace: Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared: Features shared for referencing among calculations.
org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store: A collection of named-Features.
org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean: Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter: Base classes for comparing a channel to another type.
org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator: Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error: Specific exception types that can be thrown in this module.
org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init: Initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment: Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange: Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object: Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider: Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack: A provider of Stacks.
org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment: Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary: Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object: Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial: Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange: Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction: Beans to specify a direction.
org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold: Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation: Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance: Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent: Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area: Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume: Converting quantities of volume between units.
org.anchoranalysis.image.core.bufferedimage - package org.anchoranalysis.image.core.bufferedimage: Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel: The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert: Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached: Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory: Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.contour - package org.anchoranalysis.image.core.contour: Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions: Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.dimensions.size.suggestion - package org.anchoranalysis.image.core.dimensions.size.suggestion: Suggestions on a size for an image.
org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask: An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine: Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge: Merges two or more entities.
org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object: The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label: Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties: An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale: Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.scale.method - package org.anchoranalysis.image.core.object.scale.method: Scaling elements with an associated ObjectMask either collectively or independently.
org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points: Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack: Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named - package org.anchoranalysis.image.core.stack.named: A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean: Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator: Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram: Features that operate on a Histogram.
org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection: Features that operate on a ObjectCollection.
org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair: Features that operate on a pair of ObjectMasks.
org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single: Features that operate on a single ObjectMask.
org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical: Features that convert to/from physical spatial units (e.g.
org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation: Reusable implementations of CalculationPart related to images.
org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator: Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged: A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input: Image-related implementations of FeatureInput.
org.anchoranalysis.image.io - package org.anchoranalysis.image.io: Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel: Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw: How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature: Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine: Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.metadata.reader - package org.anchoranalysis.image.io.bean.stack.metadata.reader: Bean classes for reading ImageMetadata from the file-system.
org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader: Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer: Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input: Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.input.series - package org.anchoranalysis.image.io.channel.input.series: Non-bean classes for reading a series of Channels from the filesystem.
org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output: Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input: Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output: Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object: Non-bean classes for reading / writing an ObjectCollection from and to the filesystem.
org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input: Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale: Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5: Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask: Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb: Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack: Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input: Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output: Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box: Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator: Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.io.stack.time - package org.anchoranalysis.image.io.stack.time: A time-sequence of Stacks.
org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel: Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic: Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary: The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected: Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values: Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max: Buffer for performing a Maximum Intensity Projection.
org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean: Buffer for performing a mean intensity projection.
org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive: Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice: A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert: Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.bufferedimage - package org.anchoranalysis.image.voxel.convert.bufferedimage: Converts anchor data-structures to the BufferedImage used by Java's AWT.
org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2: Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype: The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter: Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory: Creates new instances of Voxels and VoxelsUntyped with specific data-types.
org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator: Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator: Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting: Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor: Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate: Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process: Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer: Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel: Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count: Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological: Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline: Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object: The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological: Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate: Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics: Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder: Thresholding operations on voxels.
org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats: Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean: Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options: User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
org.anchoranalysis.io.bioformats.bean.writer - package org.anchoranalysis.io.bioformats.bean.writer: Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert: Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat: Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint: Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort: Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.bioformats.metadata - package org.anchoranalysis.io.bioformats.metadata: Reading metadata information from files using EXIF and/or other metadata headers.
org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator: Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection: Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined: Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence: Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern: A particular naming pattern files follow when outputted.
org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized: Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular: Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text: Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml: Generators for writing XML data.
org.anchoranalysis.io.imagej.bean - package org.anchoranalysis.io.imagej.bean
org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer: Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert: Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.imagej.interpolator - package org.anchoranalysis.io.imagej.interpolator: Image interpolation when scaling using ImageJ.
org.anchoranalysis.io.input - package org.anchoranalysis.io.input: Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean: Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary: Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files: Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer: Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path: Beans pertaining to manipulating and matching against file-paths.
org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher: Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider: Methods to provide a single file-path.
org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv: Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file: Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path: Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher: Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest: A manifest that records what outputs occur and where they occur.
org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer: Classes to read manifests from the file-system.
org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory: Entities to indicate a directory in the manifest.
org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced: Classes related to a directory that has a particular sequence of outputted filenames.
org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file: Entities to indicate a file and its role in the manifest.
org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder: Methods to search through a manifest-file to find outputs matching certain conditions.
org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match: Predicates that are useful for matching against particular type of objects in finders.
org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder: Makes a record of each file/subdirectory written as output.
org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype: Predictable patterns of indexes as used in sets of outputted files.
org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean: Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled: Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer: Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules: Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled: Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi: Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single: Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error: Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle: Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter: Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory: BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer: Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded: Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer: Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml: Outputting XML to the file-system.
org.anchoranalysis.launcher - package org.anchoranalysis.launcher: Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParams for loading a Experiment.
org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path: SelectParams for loading a Optional<Path> for inputs, outputs or tasks.
org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert: Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options: A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process: Adding/removing/changing the arguments (input and output) from the experiment via command-line-options.
org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources: Reading and integrating resources for the launcher.
org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run: Parses command-line arguments and runs an experiment.
org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks: Loading and displaying pre-defined tasks.
org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic: Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation: Solving or manipulating equations.
org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram: The Histogram data class and related operations.
org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization: Mathemathical optimization algorithms.
org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation: Different kinds of binary-relations.
org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics: Data structures and algorithms to calculate statistics.
org.anchoranalysis.math.statistics.moment - package org.anchoranalysis.math.statistics.moment: Calculates first and second image moments from a covariance matrix of points.
org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean: Beans pertaining to marked-point-processes.
org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound: Lower and upper limits set around variables.
org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation: Bounds on how to rotate an entity in Euclidean space.
org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark: Beans generally related to Marks.
org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory: Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points: Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter: Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer: Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider: Implementations of Provider involving Marks.
org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap: Voxel subregions of Marks.
org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria: Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element: Implementations and helper classes for calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme: Creating EnergySchemes.
org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark: Features calculated on a Mark.
org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection: Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy: Non-bean classes pertaining to calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks: Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved: Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme: Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error: Exceptions relating to Features involving classes from anchor-mpp.
org.anchoranalysis.mpp.feature.input - package org.anchoranalysis.mpp.feature.input: Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark: Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index: Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory: Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init: Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input: Beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature: Beans for communicating feature-values from data-structures in human-readable manner.
org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input: Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks: Non-beans to help write visualization of Marks to the filesystem.
org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator: Generator base classes to help write visualization of Marks to the filesystem.
org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output: Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark: Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic: Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points: Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized: A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap: Calculating overlaps between two Marks.
org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay: Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair: Pairs of Marks.
org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer: Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error: Recording errors related to proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean: Beans for segmentation algorithms related to marked-point-processes.
org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define: DefineOutputter and its sub-classes.
org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization: Schemes for finding optima (minima or maxima) via optimization.
org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback: Providing feedback on the progress of a OptimizationScheme.
org.anchoranalysis.mpp.segment.bean.optimization.kernel - package org.anchoranalysis.mpp.segment.bean.optimization.kernel: Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination: In which circumstances to terminate an OptimizationScheme that is underway.
org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define: Non-bean classes used in org.anchoranalysis.mpp.segment.bean.define.
org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization: Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.
org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback: Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.feedback.
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate: Aggregating optimization feedback over time.
org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period: Collecting optimization feedback periodically.
org.anchoranalysis.mpp.segment.optimization.kernel - package org.anchoranalysis.mpp.segment.optimization.kernel: Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.kernel.
org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step: Describes an individual step in the optimization.
org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer: Mapping one type of optimization state to another.
org.anchoranalysis.overlay - package org.anchoranalysis.overlay: Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean: Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection: Collections of Overlays.
org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier: Uniquely identifying an Overlay.
org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object: An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled: Creates a scaled version of ObjectMask to use as an overlay.
org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer: Drawing an overlay on an image.
org.anchoranalysis.plot - package org.anchoranalysis.plot: Plotting data on charts.
org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean: Beans for plotting.
org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme: Color schemes associated with plots.
org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index: Non-bean plot definitions.
org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate: Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer: Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison: Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file: FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label: A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy: Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison: Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.annotation.counter - package org.anchoranalysis.plugin.annotation.counter: Utility classes for counting images incrementally.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction: Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider: Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define: Implementations of DefineAdderBean that use FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider: Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold: Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur: Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert: Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider: Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign: Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert: Implementations of ChannelProvider that converts a Channel from one voxel-type to another.
org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Implementations of ChannelProvider that calculate the gradient of a Channel's voxels in one or more dimensions.
org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask: Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object: Implementations of ChannelProvider that involve conversion from or application of ObjectMasks.
org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score: Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice: Implementations of ChannelProvider that process 3D channels slice-by-slice.
org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider: Implementations of ColorProvider.
org.anchoranalysis.plugin.image.bean.dictionary - package org.anchoranalysis.plugin.image.bean.dictionary: Beans pertaining to Dictionary.
org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider: Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider: Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold: Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider: Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine: Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert: Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment: Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice: Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter: Implementations of ObjectFilter.
org.anchoranalysis.plugin.image.bean.object.filter.collective - package org.anchoranalysis.plugin.image.bean.object.filter.collective: Implementations of ObjectFilter that assess each element in a collection collectively.
org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine: Implementations of ObjectFilter that combine two or more other ObjectFilters.
org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent: Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match: Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider: Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected: Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature: Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter: Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask: Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge: Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological: Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment: Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice: Implementations of ObjectCollectionProvider involving z-slice processing.
org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split: Implementations of ObjectCollectionProvider involving splitting objects into smaller objects.
org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel: Implementations of SegmentChannelIntoObjects.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima: Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction: Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong: Implementation of a Watershed transformation based on Yeong et al.
org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce: Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale: Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary: Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider: Implementations of StackProvider.
org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color: Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot: Implementations of StackProvider that perform plotting.
org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object: Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack: Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel: Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions: Features that are calculated from Dimensions.
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Implementations of FeatureHistogram that calculate statistics.
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Implementations of FeatureHistogram that perform thresholding.
org.anchoranalysis.plugin.image.feature.bean.list - package org.anchoranalysis.plugin.image.feature.bean.list: Implementations of FeatureListProvider.
org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair: Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute: Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.image.feature.bean.metadata - package org.anchoranalysis.plugin.image.feature.bean.metadata: Implementations of FeatureImageMetadata.
org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological: Beans that affects how morphological operations occur.
org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection: Implementations of FeatureObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine: Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair: Features from pairs of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Features that calculate the degree of overlap between two ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: Features that calculate how many other objects an ObjectMask directly neighbors.
org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single: Implementations of FeatureSingleObject.
org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border: Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox: Implementations of FeatureSingleObject that consider an object's bounding-box.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Implementations of FeatureSingleObject that measure an object's gradient from corresponding Channels storing the gradient.
org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Implementations of FeatureSingleObject based on calculating image moments, with or without image intensity.
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: Implementations of FeatureSingleObject that implement morphological operations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape: Implementations of FeatureSingleObject that measure the shape of the ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared: Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Implementations of FeatureSingleObject that processes an object slice-by-slice in the z-dimension.
org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface: Implementations of FeatureSingleObject that measures aspects of the surface of an ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical: Beans involving physical units for measurement.
org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score: Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared: Beans involving SharedObjects.
org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object: Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity: Implementations of FeatureStack or other features that involve processing a Stack.
org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object: Implementations of FeatureStack that process an ObjectCollection.
org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object: Non-bean classes that help calculate features from ObjectMasks.
org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate: Implementations of CalculationPart as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single: Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological: Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation: Implementations of CalculationPart that process Stacks as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity: Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level: Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object: Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge: Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition: Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority: Assigning priority when merging ObjectMasks.
org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider: Non-bean classes pertaining to Providers.
org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice: Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding: Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean: A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature: Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source: Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format: Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped: Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster: Task(s) to calculate the mean of channels grouped together.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller: Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale: Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment: Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice: Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature: Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator: Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped: Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller: Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment: Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack: Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail: Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider: Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter: Filters using ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments: Non-linear filters using ImageJ that use the statistical moments of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank: Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define: Implementations of DefineAdderBean that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider: Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider: Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment: Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider: Implementations of StackProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold: Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider: Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask: Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map: Implementations of ChannelMap.
org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method: Methods for copying files on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming - package org.anchoranalysis.plugin.io.bean.file.copy.naming: Rules for preserving or changing the naming of files when copying on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster - package org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Implementations of CopyFilesNaming that perform clustering of files.
org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group: Grouping files together so that they collectively represent a single entity.
org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check: Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser: Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer: Implementations of FileNamer.
org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan: Implementations of FileNamer that look for a pattern across many files.
org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path: Beans to specify a file-path.
org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer: Implementations of PathPrefixer.
org.anchoranalysis.plugin.io.bean.file.pattern - package org.anchoranalysis.plugin.io.bean.file.pattern: Extracting a pattern from a file-path.
org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider: Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input: Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel: InputManagers that accept a set of named-channels.
org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files: InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider: Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter: Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest: Implementations of InputManager that read a serialized Manifest-file.
org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack: Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.metadata.header - package org.anchoranalysis.plugin.io.bean.metadata.header: Different types of image-file-formats whose headers can provide ImageMetadata.
org.anchoranalysis.plugin.io.bean.metadata.reader - package org.anchoranalysis.plugin.io.bean.metadata.reader: Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive: Implementations of DerivePath.
org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader: Implementations of StackReader.
org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer: Implementations of StackWriter.
org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer: Summarizing a set of elements into a descriptive-string.
org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image: Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input: Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path: Implementations of Summarizer that summarize generically Paths.
org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task: Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.io.file.copy - package org.anchoranalysis.plugin.io.file.copy: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path: Non-bean classes to help in processing paths.
org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.manifest.
org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile: Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer: Buffers used in org.anchoranalysis.plugin.io.multifile.
org.anchoranalysis.plugin.io.naming.interval - package org.anchoranalysis.plugin.io.naming.interval: How to write parts of a time-interval in a file-name.
org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared: Objects used in shared-state in Tasks in this plugin.
org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml: Reading and writing metadata XML.
org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier: Beans that perform classification in some way.
org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster: Beans that perform clustering in some way.
org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria: Implementations of AddCriteriaPair involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound: Implementations of MarkBoundsProvider.
org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check: Implementations of CheckMark.
org.anchoranalysis.plugin.mpp.bean.contour - package org.anchoranalysis.plugin.mpp.bean.contour: Retrieving the contour outline pixels along the exterior outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler: The VisitScheduler and related classes, as used in TraverseOuterContourOnImage.
org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define: Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider: Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection: Implementations of MarkCollectionProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single: Implementations of MarkProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection: Implementations of MarkFromCollectionProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge: Implementations of MarkMergeProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation: Implementations of OrientationProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points: Implementations of PointsProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points.contour - package org.anchoranalysis.plugin.mpp.bean.proposer.points.contour: Finding a point on the external outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation: PointsFromOrientationProposer and implementations.
org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position: Implementations of PositionProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii: Implementations of RadiiProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar: Implementations of ScalarProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split: Implementations of MarkSplitProposer.
org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection: Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single: Implementations of SingleMarkProvider.
org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region: Implementations of MarkRegion.
org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary: Implementations of BinarySegmentation involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider: Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.mpp.contour - package org.anchoranalysis.plugin.mpp.contour: Performs a walk on every voxel on the contour of an object-mask.
org.anchoranalysis.plugin.mpp.contour.distance - package org.anchoranalysis.plugin.mpp.contour.distance: A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
org.anchoranalysis.plugin.mpp.contour.path - package org.anchoranalysis.plugin.mpp.contour.path: A set of contiguously neighboring points along the outline of an object.
org.anchoranalysis.plugin.mpp.contour.path.merge - package org.anchoranalysis.plugin.mpp.contour.path.merge: Merging multiple ContiguousVoxelPath together.
org.anchoranalysis.plugin.mpp.contour.path.merge.strategy - package org.anchoranalysis.plugin.mpp.contour.path.merge.strategy: Strategies on which ContiguousVoxelPath should be prioritized for merging.
org.anchoranalysis.plugin.mpp.experiment.bean.convert - package org.anchoranalysis.plugin.mpp.experiment.bean.convert: Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define: Tasks that use a DefineOutputter or related classes.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report: Implementations of ReportFeatureForManifest.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task: Tasks that calculate and export ReportFeatures.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source: Implementations of FeatureSource.
org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects: Tasks involving ObjectMasks.
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition: Defining columns used in ExportObjectsFromCSV.
org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment: Tasks that segment an image to produce a MarkCollection.
org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects: Non-bean classes used in org.anchoranalysis.plugin.mpp.experiment.bean.objects.
org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv: Reading rows from a CSV file.
org.anchoranalysis.plugin.mpp.experiment.shared - package org.anchoranalysis.plugin.mpp.experiment.shared: Shared-state use across tasks in this JAR.
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection: Implementations of FeatureMarkCollection.
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction: Implementations of FeatureMark to measure direction.
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii: Implementations of FeatureMark to measure or calculate radii.
org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region: Implementations of FeatureMark to measure regions of Marks.
org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all: Implementations of FeatureAllMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind: Implementations of FeatureSingleMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair: Implementations of FeaturePairMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Implementations of FeaturePairMemo to measure distance between Marks.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap: Implementations of FeaturePairMemo to measure overlap between Marks.
org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit: Beans to convert between units.
org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap: Implementations of CalculationPart to calculate overlap between two entities.
org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing: Implementations of AnnealScheme.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark: Implementations of KernelBirth that are dependent.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent: Implementations of KernelBirth that are independent.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized: Implementations of KernelBirth that are independent but use the voxelized state of a Mark.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer: Implementations of KernelProposerOption.
org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks: Beans to perform segmentation involving Marks and related classes.
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual: Implementations of StateTransformerBean involving DualVoxelizedMarks.
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition: Implementations of StateTransformerBean involving MarksFromPartition.
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized: Implementations of StateTransformerBean involving VoxelizedMarksWithEnergy.
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight: Deriving a weight for a Mark.
org.anchoranalysis.plugin.mpp.segment.bean.optimization - package org.anchoranalysis.plugin.mpp.segment.bean.optimization: Beans related to performing optimization with marked-point-processes.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract: Implementations of ExtractScoreSize.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: KernelStateBridge and implementations.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: AssignMode and implementations.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Implementations of FeedbackReceiverBean.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme: Implementations of OptimizationScheme.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter: Implementations of StateReporter.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination: Implementations of TerminationCondition.
org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner: Implementations of KernelAssigner.
org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater: KernelUpdater and implementations.
org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization: Non-bean classes to help with optimization in org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages.
org.anchoranalysis.plugin.mpp.segment.shared - package org.anchoranalysis.plugin.mpp.segment.shared: Stared-state for segmentation tasks involving mark-point-processes.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn: Decodes the outputted tensors from a Mask R-CNN implementation.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text
org.anchoranalysis.plugin.onnx.bean.object.segment.stack - package org.anchoranalysis.plugin.onnx.bean.object.segment.stack
org.anchoranalysis.plugin.onnx.model - package org.anchoranalysis.plugin.onnx.model
org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv: Plugins that call OpenCV.
org.anchoranalysis.plugin.opencv.bean.color - package org.anchoranalysis.plugin.opencv.bean.color: Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature: Extracting features using OpenCV.
org.anchoranalysis.plugin.opencv.bean.interpolate - package org.anchoranalysis.plugin.opencv.bean.interpolate: Interpolation beans that use OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack: Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.bean.stack - package org.anchoranalysis.plugin.opencv.bean.stack: Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert: Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.opencv.interpolator - package org.anchoranalysis.plugin.opencv.interpolator: Interpolation non-beans that use OpenCV.
org.anchoranalysis.plugin.opencv.segment - package org.anchoranalysis.plugin.opencv.segment: Non-bean classes pertaining to segmentation.
org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean: Features that combine or convert other features in a generic way.
org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic: Arithmetic involving features.
org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional: Conditional operations involving features.
org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list: Operations that extract a single value from a list of features.
org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range: Features that compare against a range of values.
org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace: Replaces particular values if they are returned from a feature.
org.anchoranalysis.plugin.operator.feature.bean.statistics - package org.anchoranalysis.plugin.operator.feature.bean.statistics: Converts feature values based upon a statistical measure of distribution.
org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical: Converting to/from physical units.
org.anchoranalysis.plugin.operator.feature.statistics - package org.anchoranalysis.plugin.operator.feature.statistics: Non-bean statistical operations.
org.anchoranalysis.plugin.points.bean - package org.anchoranalysis.plugin.points.bean: Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull - package org.anchoranalysis.plugin.points.bean.convexhull: Convex hull operations.
org.anchoranalysis.plugin.points.bean.feature - package org.anchoranalysis.plugin.points.bean.feature: Features related to points and fitting points to conics.
org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter: Fitting geometric structures to points.
org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse: CalculationPart related to fitting ellipses to points by least-squares.
org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid: CalculationPart related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull: Non-bean convex hull operations.
org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment: Quickly defining experiments via several assumptions, including particular file-paths.
org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive: Deriving paths from existing paths as helpful to quickly defined experiments.
org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input: Specifying inputs when quickly defining an experiment.
org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend: Appending other entities to inputs when quickly defining experiments.
org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure: Specifying a structure of subdirectories and filenames when quickly defining an experiment.
org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis: Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box: Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.orientation - package org.anchoranalysis.spatial.orientation: Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point: A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer: Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree: R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale: How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test - package org.anchoranalysis.test: Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment: Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher: Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.experiment.task - package org.anchoranalysis.test.experiment.task: Helper classes to execute Tasks in tests.
org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature: Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins: Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature: A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects: Fixtures for creating object-masks and related feature-inputs.
Orientation - Class in org.anchoranalysis.image.io.bean.object.draw: Writes a line through the midpoint illustrating the orientation of the object
Orientation() - Constructor for class Orientation
Orientation - Class in org.anchoranalysis.spatial.orientation: The orientation (direction) in 2D or 3D Euclidean space.
Orientation() - Constructor for class Orientation
Orientation2D - Class in org.anchoranalysis.spatial.orientation: A simple angular orientation the 2D plane, relative to the x-axis.
Orientation2D(double) - Constructor for class Orientation2D
Orientation2D() - Constructor for class Orientation2D
Orientation3DEulerAngles - Class in org.anchoranalysis.spatial.orientation: An orientation using three angle parameters for the rotation.
Orientation3DEulerAngles(double, double, double) - Constructor for class Orientation3DEulerAngles
OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single: Proposes both an orientation and radii for a ConicBase
OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class OrientationAndRadiiProposer
OrientationAxisAngle - Class in org.anchoranalysis.spatial.orientation: An orientation in axis-angle representation.
OrientationAxisAngle(Vector3d, double) - Constructor for class OrientationAxisAngle
OrientationChange - Enum in org.anchoranalysis.image.core.dimensions: Changes orientation of an image in the XY plane.
OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
OrientationProposer() - Constructor for class OrientationProposer
OrientationReader - Class in org.anchoranalysis.io.bioformats.metadata: Reads the image-orientation from EXIF metadata, if specified in an image-file.
OrientationRotationMatrix - Class in org.anchoranalysis.spatial.orientation: Orients an object by rotating anti-clockwise with an explicit RotationMatrix.
OrientationRotationMatrix() - Constructor for class OrientationRotationMatrix
OrientationRotationMatrix(RotationMatrix) - Constructor for class OrientationRotationMatrix
otherVertex(V) - Method in class TypedEdge: The other vertex on the edge
Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Performs auto-thresholding using Otsu's method.
Otsu() - Constructor for class Otsu
OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Similar to Otsu, but weighs the variances differently of background and foreground.
OtsuWeighted() - Constructor for class OtsuWeighted
OtsuWeighted(double, double) - Constructor for class OtsuWeighted
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixer: Provides a prefix which can be prepended to all output files.
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class Rooted
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve: Provides a prefix which can be prepended to all output files.
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IncrementingNumber
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve: Determines the out-file prefix from a path
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class DirectoryStructure
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class FromDescriptiveName
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IfIncrementingNumberRequested
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class LastDirectoryAsPrefix
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathRegEx
outgoingEdgesFor(V) - Method in class GraphWithPayload: All outgoing edges for a given vertex.
Outline - Class in org.anchoranalysis.image.io.bean.object.draw: Draws the outline of each object-mask.
Outline() - Constructor for class Outline
Outline(int) - Constructor for class Outline
Outline(int, boolean) - Constructor for class Outline
OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline: Sets voxels on the outline of an object to be on and otherwise off.
OutlineKernel() - Constructor for class OutlineKernel
OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline: A base class for kernels that find the outline of an ObjectMask.
OutlineKernelBase() - Constructor for class OutlineKernelBase: Default constructor.
OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
OutlineKernelBase() - Constructor for class OutlineKernelBase
OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline: Outputs the outline of an object-mask, but only for voxels on the exterior which neighbor a binary-mask.
OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class OutlineKernelNeighborMatchValue: Creates for an object.
OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
OutlinePreserveRelativeSize() - Constructor for class OutlinePreserveRelativeSize
outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects on a background using a single color for all objects.
outlineVariedColors(int, int, DisplayStack) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects on a background using varied colors for the objects.
outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects on a background using varied colors for the objects.
outlineWithColorIndex(int, ColorIndex) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects using a particular color-index.
output() - Method in class ExecutionArguments: Arguments to help specify the outputs from the experiment.
output(InputOutputContext) - Method in class OutputFeatureTable: Outputs the feature-table.
output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class NamedStacksOutputter: Writes all or a subset from a set of named-stacks to a directory as a raster.
output(String, boolean) - Method in class NamedProviderOutputter: Outputs the entities using a particular output-name.
OUTPUT_BY_GROUP - Static variable in class CompareAnnotations
OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class FeatureOutputNames: If not otherwise specified, the output name for a non-aggregated CSV of the results.
OUTPUT_ENERGY_STACK_DIRECTORY - Static variable in class EnergyStackWriter
OUTPUT_EXECUTION_TIME - Static variable in class OutputExperiment
OUTPUT_FEATURE_TABLE - Static variable in class OutputFeatureTable
OUTPUT_MANIFEST - Static variable in class OutputExperiment
OUTPUT_MANIFEST - Static variable in class Task
OUTPUT_RESULTS - Static variable in class ExportFeatures
OUTPUT_SUFFIX_AGGREGATED - Static variable in class FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for aggregated features
OUTPUT_SUFFIX_AGGREGATED_GROUP - Static variable in class FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for aggregated grouped features
OUTPUT_SUFFIX_GROUP - Static variable in class FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for grouped features
OUTPUT_THUMBNAILS - Static variable in class FeatureExporter: The output-name for writing thumbnails.
outputAfterAllTasksAreExecuted(Outputter) - Method in interface ExperimentState
outputAfterAllTasksAreExecuted(Outputter) - Method in class SegmentMarksState
OutputArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's output in addition to its bean specification.
OutputArguments() - Constructor for class OutputArguments
outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface ExperimentState
outputBeforeAnyTasksAreExecuted(Outputter) - Method in class SegmentMarksState
OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error: When an output-directory already exists.
OutputDirectoryAlreadyExistsException(String) - Constructor for exception OutputDirectoryAlreadyExistsException
OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Whether a particular output, identified by a textual name, is enabled or not.
OutputEnabled() - Constructor for class OutputEnabled
OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded: Additional output-names to enable or disable from an existing set of output-enabled rules.
OutputEnabledDelta() - Constructor for class OutputEnabledDelta
OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled: A specific set of first-level outputs are enabled, to which more can be added.
OutputEnabledMutable(String...) - Constructor for class OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules: Bean that specifies an implementation of MultiLevelOutputEnabled.
OutputEnabledRules() - Constructor for class OutputEnabledRules
OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules: Base class for an OutputEnabledRules that specifies particular output-names for first and second levels.
OutputEnableRulesSpecify(StringSet) - Constructor for class OutputEnableRulesSpecify: Create with a specific set of first-level output names.
OutputEnableRulesSpecify() - Constructor for class OutputEnableRulesSpecify
OutputExperiment - Class in org.anchoranalysis.experiment.bean.io: An experiment that uses a OutputManager to specify the outputting of results.
OutputExperiment() - Constructor for class OutputExperiment
OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for outputs.
OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature: Specifies a table of feature-calculations on objects.
OutputFeatureTable() - Constructor for class OutputFeatureTable
outputFormatString() - Method in class IndexableOutputNameStyle
outputFormatString() - Method in class IntegerSuffixOutputNameStyle
outputFormatString() - Method in class StringSuffixOutputNameStyle
outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class GroupMapByName: Outputs the "grouped" data to the filesystem
outputHeaderToWriter(PrintWriter, String) - Method in class AggIDCounter
outputHeaderToWriter(PrintWriter) - Method in class Aggregator
OutputManager - Class in org.anchoranalysis.io.output.bean: Responsible for making decisions on where output goes and what form it takes.
OutputManager() - Constructor for class OutputManager
outputName(String) - Static method in class FileMatch: Match a file whose output-name matches a specific value.
outputNameForGroups() - Method in class GroupedStackBase: The first-level output-name used for determining if groups are written.
outputNameForGroups() - Method in class ExportImageHistograms
outputNameForGroups() - Method in class GroupedMeanChannelTask
outputNames() - Method in class FeatureOutputMetadata: Names for any outputs produced by FeatureCalculationResults.
OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
OutputNameStyle(String) - Constructor for class OutputNameStyle
OutputNameStyle() - Constructor for class OutputNameStyle
OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern: A particular naming pattern files follow when outputted.
OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class OutputPattern
OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing integer index.
OutputPatternIntegerSuffix(String, boolean) - Constructor for class OutputPatternIntegerSuffix: Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
OutputPatternIntegerSuffix(String, String) - Constructor for class OutputPatternIntegerSuffix: Creates in a subdirectory, using the output-name as the subdirectory name, and a specific prefix.
OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, boolean) but with additional options on the manifest-folder description and whether to check outputs against rules.
OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, String) but with additional options about the number of digits, the manifest-folder description and whether to check outputs against rules.
OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix: Creates with a full set of flexibility about how the filename appears and whether a subdirectory is used.
OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing string index.
OutputPatternStringSuffix(String, boolean) - Constructor for class OutputPatternStringSuffix: Creates without a prefix.
OutputPatternStringSuffix(String, boolean, String) - Constructor for class OutputPatternStringSuffix: Creates with a prefix.
OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer: Arguments influencing into which directory outputs are written, and how identifiers are expressed.
OutputPrefixerSettings() - Constructor for class OutputPrefixerSettings
OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files using whatever prefix is assigned to an input by the OutputManager as the file-name, adding the same extension as the source file.
OutputPrefixWithExtension() - Constructor for class OutputPrefixWithExtension
outputSelectParam(CommandLine) - Static method in class SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an output manager a directory, set as the outputDirectory in the input-context
outputsEnabled() - Method in class Outputter
OutputSequence - Interface in org.anchoranalysis.io.generator.sequence: A sequence of elements that are written to the same directory.
OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence: Creates and starts a OutputSequence with a particular generator and context.
OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class OutputSequenceFactory
OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator, where each output increments an index by one in the filename.
OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class OutputSequenceIncrementing
OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator with non-incrementing indexes for each output.
OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output: Creates OutputSequence of different kinds for writing stacks to a directory.
outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class DefineOutputter
OutputtedFile - Class in org.anchoranalysis.io.manifest.file: An entry in a Manifest for an outputted file from an experiment.
OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class OutputtedFile
OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class OutputtedFile
Outputter - Class in org.anchoranalysis.io.output.outputter: Like OutputterChecked but exceptions are reported in a ErrorReporter.
Outputter(OutputterChecked, ErrorReporter) - Constructor for class Outputter
OutputterChecked - Class in org.anchoranalysis.io.output.outputter: A particular directory on the filesystem in which outputting can occur.
OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define: Directories into which collections of different types of objects are written to in a define experiment
OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory: The directory and prefix an outputter writes to.
OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class OutputterTarget
outputToWriter(PrintWriter) - Method in class AggIDCounter
outputToWriter(PrintWriter) - Method in class Aggregator
OutputWriteContext - Class in org.anchoranalysis.io.output.outputter: Settings and user-arguments for writing files.
OutputWriteContext() - Constructor for class OutputWriteContext: Create with default state, including no default beans assigned.
OutputWriteContext(OutputWriteSettings) - Constructor for class OutputWriteContext: Create from OutputWriteSettings and otherwise with defaults.
OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>, ExecutionTimeRecorder) - Constructor for class OutputWriteContext
OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
OutputWriteFailedException(String) - Constructor for exception OutputWriteFailedException
OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception OutputWriteFailedException
OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception OutputWriteFailedException
OutputWriteFailedException(Throwable) - Constructor for exception OutputWriteFailedException
OutputWriteSettings - Class in org.anchoranalysis.io.output.bean: Settings for how to write output, including default writers.
OutputWriteSettings() - Constructor for class OutputWriteSettings
OutsideKernelPolicy - Enum in org.anchoranalysis.image.voxel.kernel: How to handle voxels whose neighbors are outside the scene.
OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
OutsideRange() - Constructor for class OutsideRange
overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper: Iterates over all voxels.
overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper: Iterates over only voxels contained within a bounding-box.
overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class IterateKernelHelper: Iterates over only voxels contained within a bounding-box until a predicate is matched on a voxel.
OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapMaskBase() - Constructor for class OverlapMaskBase
OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapMIPBase() - Constructor for class OverlapMIPBase
OverlapNumberVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapNumberVoxelsMask() - Constructor for class OverlapNumberVoxelsMask
OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapNumVoxels() - Constructor for class OverlapNumVoxels
overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeaturePairMemoSingleRegion
overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMIPBase
OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label: An object-mask that is founded to overlap with another during labelling.
OverlappingObject(T, ObjectMask) - Constructor for class OverlappingObject
OverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment: Pairs an ObjectMask in one set with an ObjectMask in another, if deemed to overlap sufficiently.
OverlappingObjects() - Constructor for class OverlappingObjects
OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapRatio() - Constructor for class OverlapRatio
OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapRatioMask() - Constructor for class OverlapRatioMask
OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Expresses the number of intersecting pixels between two objects as a ratio to something else (denominator)
OverlapRelative() - Constructor for class OverlapRelative
OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToFirst() - Constructor for class OverlapRelativeToFirst
OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Overlap ratio to the maximum number of pixels
OverlapRelativeToMaxVolume() - Constructor for class OverlapRelativeToMaxVolume
OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToMerged() - Constructor for class OverlapRelativeToMerged
OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToSecond() - Constructor for class OverlapRelativeToSecond
OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class OverlapUtilities
overlapWithGlobalMask(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class OverlapUtilities: Counts the number of overlapping voxels between two VoxelizedMarkMemo
Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange: Overlays one image on the other.
Overlay() - Constructor for class Overlay
Overlay(String, String, String) - Constructor for class Overlay
Overlay - Class in org.anchoranalysis.overlay: An entity that will eventually be drawn on top of an image.
Overlay() - Constructor for class Overlay
OverlayCollection - Class in org.anchoranalysis.overlay.collection
OverlayCollection() - Constructor for class OverlayCollection
OverlayCollection(Stream<Overlay>) - Constructor for class OverlayCollection
OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay: Two-way factory.
OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection: Two-way factory.
OverlayMark - Class in org.anchoranalysis.mpp.overlay
OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class OverlayMark
OverlayObjectMask - Class in org.anchoranalysis.overlay.object
OverlayObjectMask(ObjectMask, int) - Constructor for class OverlayObjectMask
OverlayProperties - Class in org.anchoranalysis.overlay
OverlayProperties() - Constructor for class OverlayProperties

P

Padding - Class in org.anchoranalysis.image.bean.spatial

Padding (whitespace of certain extent) placed around an object in XY direction and in Z direction.

Padding() - Constructor for class Padding

paired(boolean) - Method in interface Assignment

The items that are paired for a particular set.

paired(boolean) - Method in class ObjectVoxelIntersection

paired(boolean) - Method in class OverlappingObjects

PairedWithMask - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared

Evaluates the object as a pair-feature together with the binary-mask from the shared objects.

PairedWithMask() - Constructor for class PairedWithMask

PairNeighbors - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine

Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.

PairNeighbors() - Constructor for class PairNeighbors

PairPxlMarkMemo - Class in org.anchoranalysis.mpp.pair

PairPxlMarkMemo(VoxelizedMarkMemo, VoxelizedMarkMemo) - Constructor for class PairPxlMarkMemo

PairsTableCalculator - Class in org.anchoranalysis.image.feature.calculator.merged

A feature-session to evaluate pairs of objects.

PairsTableCalculator(MergedPairsFeatures) - Constructor for class PairsTableCalculator

PairsTableCalculator(MergedPairsFeatures, MergedPairsInclude, boolean) - Constructor for class PairsTableCalculator

Pairwise - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition

Pairwise() - Constructor for class Pairwise

ParallelProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor

Executes jobs in parallel

ParallelProcessor() - Constructor for class ParallelProcessor

ParametersExperiment - Class in org.anchoranalysis.experiment.task

Parameters for executing a task, when the manifest, log etc.

ParametersExperiment(ExecutionArguments, String, Optional<Manifest>, OutputterChecked, PathPrefixer, ExperimentFeedbackContext) - Constructor for class ParametersExperiment

parametersOnly() - Static method in class NamedFeatureStoreFactory

The custom-names of the features are derived only from their parameters, but not their name.

ParametersUnbound<T,S> - Class in org.anchoranalysis.experiment.task

ParametersUnbound(ParametersExperiment, T, S, boolean) - Constructor for class ParametersUnbound

ParamFromCollection<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.shared

Retrieves a parameter as stored in a Dictionary in SharedObjects.

ParamFromCollection() - Constructor for class ParamFromCollection

parse(String) - Static method in class IndexRangeNegativeFactory

Parses a string to convert it into an IndexRangeNegative.

parse(File) - Static method in class XMLParser

Parses a XML file to produce a Document.

parseAndRun(String[], LauncherConfig) - Method in class ParseArgumentsAndRunExperiment

Parses the arguments to a command-line experiment and runs an experiment.

ParseArgumentsAndRunExperiment - Class in org.anchoranalysis.launcher.run

Parses command-line arguments and runs an experiment.

ParseArgumentsAndRunExperiment(Logger) - Constructor for class ParseArgumentsAndRunExperiment

ParsedFilePathBag - Class in org.anchoranalysis.plugin.io.multifile

ParsedFilePathBag() - Constructor for class ParsedFilePathBag

parsePath(Path) - Method in class FilePathParser

parsePath(Path) - Method in class RegularExpression

PartitionedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization

Binary partition of marks into "available" and "accepted"

PartitionedMarks(MarkCollection, ToDoubleFunction) - Constructor for class PartitionedMarks

Constructor

path(String) - Static method in class DirectoryMatch

path(boolean) - Method in class FilePath

path(boolean) - Method in class RootedFilePath

path(boolean) - Method in class StaticFilePath

PATH_RESOURCES - Static variable in class TestLoader

Path to the resources directory, relative to the root of the project.

pathCreator() - Method in class OutputterTarget

PathCreator - Interface in org.anchoranalysis.io.output.path.prefixer

Converts file-paths between relative and absolute.

PathDifference - Class in org.anchoranalysis.core.system.path

Calculates the "difference" between a path and a base.

PathDifferenceException - Exception in org.anchoranalysis.core.system.path

When an error occurs calculating the difference between two file-paths.

PathDifferenceException(String) - Constructor for exception PathDifferenceException

Creates with only a message.

PathDifferenceException(String, Exception) - Constructor for exception PathDifferenceException

Creates with message and cause.

pathFor(ProvidesStackInput) - Method in class AnnotatorStrategy

The path to where an annotation file for a particular input would be located.

pathFor(ProvidesStackInput) - Method in class SinglePathStrategy

pathForBinding() - Method in class SingleFileInputBase

pathForBinding() - Method in interface InputFromManager

A path to a file from which this input originated.

pathForBinding() - Method in class InputFromManagerDelegate

pathForBinding() - Method in class MultiInput

pathForBinding() - Method in class StackWithMap

pathForBinding() - Method in class CoupledManifests

pathForBinding() - Method in class ManifestCouplingDefinition

pathForBindingForAllChannels() - Method in class NamedChannelsInputPart

pathForBindingRequired() - Method in interface InputFromManager

Like InputFromManager.pathForBinding() but throws an exception if a path isn't present.

pathForObject(int) - Static method in class HDF5PathHelper

pathFromArgument(String) - Static method in class ArgumentConverter

Converts the string passed as a command-line argument to a path.

pathFromBean(AnchorBean<?>, String) - Static method in class BeanPathCalculator

Calculates a path from the current bean.

PathFromGenerator - Class in org.anchoranalysis.plugin.annotation.bean.strategy

PathMatchConstraints - Class in org.anchoranalysis.io.input.path.matcher

Some constraints on which paths to match

PathMatchConstraints(DualPathPredicates, int) - Constructor for class PathMatchConstraints

PathMatcher - Class in org.anchoranalysis.io.input.bean.path.matcher

Matches file-paths against some kind of pattern.

PathMatcher() - Constructor for class PathMatcher

PathOperations - Class in org.anchoranalysis.plugin.io.file.copy

Helper routines for performing operations on Paths.

pathOrDirectory(String[], boolean) - Static method in class OutputFactory

If the argument is a path to a directory, then this directory is set as the default.

pathOrDirectoryOrGlobOrExtension(String[]) - Static method in class InputFactory

pathOrTaskName(String[], Path) - Static method in class TaskFactory

If the argument a name (no extension, no root, no special-chars apart from forward-slashes), then construct an automatic path to the tasks in the configuration directory.

pathOrTaskNameOrDefault(CommandLine, String, Path) - Static method in class SelectParamFactory

Can point to either a path to beanXML

PathPrefixer - Class in org.anchoranalysis.io.output.bean.path.prefixer

PathPrefixer() - Constructor for class PathPrefixer

PathPrefixerAvoidResolve - Class in org.anchoranalysis.io.output.bean.path.prefixer

A file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths

PathPrefixerAvoidResolve(String) - Constructor for class PathPrefixerAvoidResolve

PathPrefixerAvoidResolve() - Constructor for class PathPrefixerAvoidResolve

PathPrefixerContext - Class in org.anchoranalysis.io.output.path.prefixer

Context parameters provided to a link PathPrefixer.

PathPrefixerContext() - Constructor for class PathPrefixerContext

Create with default parameters.

PathPrefixerContext(boolean, OutputPrefixerSettings) - Constructor for class PathPrefixerContext

Create with specific parameters.

PathPrefixerException - Exception in org.anchoranalysis.io.output.path.prefixer

PathPrefixerException(String) - Constructor for exception PathPrefixerException

PathPrefixerException(Throwable) - Constructor for exception PathPrefixerException

PathRegEx - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer

Matches a regex against incoming file-paths to form a prefix for output

PathRegEx() - Constructor for class PathRegEx

pathRelativeProperties() - Method in class LauncherConfig

Path to a property file that defines a relative-path to the default experiment in bean XML.

PathSupplier - Interface in org.anchoranalysis.io.input.path

pattern() - Method in enum DateStyle

Derives a pattern for the formatter for the particular date-style.

PatternSpan - Class in org.anchoranalysis.plugin.io.bean.file.namer.patternspan

Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the name.

PatternSpan() - Constructor for class PatternSpan

patternWithDate(DateStyle) - Method in enum TimeStyle

Derives a formatter for the particular date AND time-style.

PayloadCalculator - Interface in org.anchoranalysis.plugin.image.object.merge

percentLeftAssigned() - Method in class OverlappingObjects

The percentage of objects in the left set that have been paired.

percentRightAssigned() - Method in class OverlappingObjects

The percentage of objects in the right set that have been paired.

performBinaryOperation(int, int) - Method in class AddConstant

performBinaryOperation(int, int) - Method in class ArithmeticWithConstantBase

The binary arithmetic operation that combines the voxel-value and the constant-value

performBinaryOperation(int, int) - Method in class MultiplyConstant

performBinaryOperation(int, int) - Method in class SubtractFromConstant

performInference(OnnxTensor, String, List<String>, CheckedFunction<List<OnnxTensor>, S, OperationFailedException>) - Method in class OnnxModel

performInference(Mat, String, List<String>, CheckedFunction<List<Mat>, S, OperationFailedException>) - Method in class OpenCVModel

periodEnd(Reporting<T>) - Method in interface PeriodReceiver

periodEnd(Reporting<T>) - Method in class PeriodReceiverList

PeriodicSubdirectoryReporter<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback

PeriodicSubdirectoryReporter() - Constructor for class PeriodicSubdirectoryReporter

PeriodReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.period

PeriodReceiverException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.period

PeriodReceiverException() - Constructor for exception PeriodReceiverException

PeriodReceiverException(String) - Constructor for exception PeriodReceiverException

PeriodReceiverException(Exception) - Constructor for exception PeriodReceiverException

PeriodReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period

PeriodReceiverList() - Constructor for class PeriodReceiverList

periodStart(Reporting<T>) - Method in interface PeriodReceiver

periodStart(Reporting<T>) - Method in class PeriodReceiverList

PeriodTriggerBank<S> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period

PeriodTriggerBank() - Constructor for class PeriodTriggerBank

Permissive - Class in org.anchoranalysis.io.output.bean.rules

Allows all output-names to be outputted in both first and second level.

Permissive() - Constructor for class Permissive

permissive() - Method in class RecordingWriters

A writer that allows all output-names, and records the written output-names

PermissiveExcept - Class in org.anchoranalysis.io.output.bean.rules

All outputs are enabled except particular ones.

PermissiveExcept(StringSet) - Constructor for class PermissiveExcept

Create with first-level output names

PermissiveExcept() - Constructor for class PermissiveExcept

PermutationAssigner - Interface in org.anchoranalysis.bean.permute.assign

Imposes a permutation on some property of a bean.

PermutationAssignerFactory - Class in org.anchoranalysis.bean.permute.assign

Creates instances of PermutationAssigner.

Permute - Class in org.anchoranalysis.plugin.image.bean.object.provider

Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection

Permute() - Constructor for class Permute

PermutedCopyCreator<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.permute

Applies a PermuteProperty to a bean to create new duplicated beans each with different permuted values.

PermutedCopyCreator(Function<T, String>, BiConsumer<T, String>) - Constructor for class PermutedCopyCreator

PermuteDivideByParam<T extends FeatureInputDictionary> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore

PermuteDivideByParam() - Constructor for class PermuteDivideByParam

PermuteFeature<S,T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

Permutes one or more properties of a Feature, so as to create a set of Features

PermuteFeature() - Constructor for class PermuteFeature

PermuteFeatureBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

Creates permutations of a feature by modifying a particular property of it in different ways.

PermuteFeatureBase() - Constructor for class PermuteFeatureBase

PermuteFeatureSequenceInteger<T extends FeatureInputDictionary> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

Permutes a property on a feature with a sequence of integers.

PermuteFeatureSequenceInteger() - Constructor for class PermuteFeatureSequenceInteger

PermuteFirstSecondOrder<T extends FeatureInputDictionary> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

PermuteFirstSecondOrder(PermuteFirstSecondOrder.CreateFirstSecondOrder<T>, double, double) - Constructor for class PermuteFirstSecondOrder

PermuteFirstSecondOrder.CreateFirstSecondOrder<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.feature.bean.list.permute

PermuteGaussianScore<T extends FeatureInputDictionary> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore

PermuteGaussianScore() - Constructor for class PermuteGaussianScore

PermuteProperty<T> - Class in org.anchoranalysis.bean.permute.property

Changes properties of an AnchorBean to one of a range of possible values.

PermuteProperty() - Constructor for class PermuteProperty

PermutePropertyDoubleSet - Class in org.anchoranalysis.bean.permute.property

Assigns each element from a set of doubles to a particular property of a bean.

PermutePropertyDoubleSet() - Constructor for class PermutePropertyDoubleSet

PermutePropertySequence<T> - Class in org.anchoranalysis.bean.permute.property

Base class for assigning a sequence of numbers to a particular property of a bean.

PermutePropertySequence() - Constructor for class PermutePropertySequence

PermutePropertySequenceDouble - Class in org.anchoranalysis.bean.permute.property

Assigns an arithmetic sequence of doubles, derived by diving an integer sequence by a divider.

PermutePropertySequenceDouble() - Constructor for class PermutePropertySequenceDouble

PermutePropertySequenceInteger - Class in org.anchoranalysis.bean.permute.property

An arithmetic sequence of integers, each directly assigned to a property during permutation.

PermutePropertySequenceInteger() - Constructor for class PermutePropertySequenceInteger

PermutePropertyStringSet - Class in org.anchoranalysis.bean.permute.property

Assigns each element from a set of strings to a particular property of a bean.

PermutePropertyStringSet() - Constructor for class PermutePropertyStringSet

PermuteZScore<T extends FeatureInputDictionary> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute

Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore

PermuteZScore() - Constructor for class PermuteZScore

Plot<T> - Class in org.anchoranalysis.plot.bean

Defines a plot as a function of data and axis-limits.

Plot() - Constructor for class Plot

PlotAxisLabels - Class in org.anchoranalysis.plot.index

Labels for x and y axis in graph

PlotAxisLabels() - Constructor for class PlotAxisLabels

PlotColorScheme - Class in org.anchoranalysis.plot.bean.colorscheme

PlotColorScheme() - Constructor for class PlotColorScheme

PlotHistogram - Class in org.anchoranalysis.plugin.image.bean.stack.provider.plot

Plots a histogram onto a stack.

PlotHistogram() - Constructor for class PlotHistogram

PlotIndexBase<T,S extends org.jfree.data.general.Dataset> - Class in org.anchoranalysis.plot.index

PlotIndexBase(String, String[]) - Constructor for class PlotIndexBase

Constructor

PlotIndexBaseCategorical<T,S extends org.jfree.data.category.CategoryDataset> - Class in org.anchoranalysis.plot.index

Base class for plots involving categorical data types.

PlotIndexBaseCategorical(String, String[], GetForSeries<T, String>, GetForSeries<T, Paint>) - Constructor for class PlotIndexBaseCategorical

PlotInstance - Class in org.anchoranalysis.plot

A Plot combined with data and parameters, ready to be displayed.

PlotInstance(JFreeChart, Optional<AxisLimits>) - Constructor for class PlotInstance

pluralize(String) - Static method in class LanguageUtilities

Given something, returns somethings.

pluralizeMaybe(long, String) - Static method in class LanguageUtilities

Returns something or somethings depending on the number.

PNG - Class in org.anchoranalysis.io.imagej.bean.stack.writer

Writes a PNG image using ImageJ.

PNG() - Constructor for class PNG

PNG - Class in org.anchoranalysis.plugin.io.bean.metadata.header

The headers found in a PNG file.

PNG() - Constructor for class PNG

point(ReadableTuple3i) - Method in class BoundingBoxContains

Is this point within the bounding-box?

Point2d - Class in org.anchoranalysis.spatial.point

A two-dimensional point of double values.

Point2d(Point2d) - Constructor for class Point2d

Creates with the same values as an existing Point2d.

Point2d(double, double) - Constructor for class Point2d

Point2d() - Constructor for class Point2d

Point2f - Class in org.anchoranalysis.spatial.point

A two-dimensional point of float values.

Point2f(float, float) - Constructor for class Point2f

Point2f() - Constructor for class Point2f

Point2i - Class in org.anchoranalysis.spatial.point

A two-dimensional point of int values.

Point2i(Point2i) - Constructor for class Point2i

Creates with the same values as an existing Point2i.

Point2i(int, int) - Constructor for class Point2i

Point2i() - Constructor for class Point2i

Point3d - Class in org.anchoranalysis.spatial.point

A three-dimensional point of double values.

Point3d(Point3f) - Constructor for class Point3d

Creates with the same values as an existing Point3d.

Point3d(Tuple3d) - Constructor for class Point3d

Creates with the same values as an existing Tuple3d.

Point3d(double, double, double) - Constructor for class Point3d

Create with values for each dimension.

Point3d() - Constructor for class Point3d

Point3f - Class in org.anchoranalysis.spatial.point

A three-dimensional point of float values.

Point3f() - Constructor for class Point3f

Creates the points with a 0 in each dimension.

Point3f(Point3f) - Constructor for class Point3f

Creates with the same values as an existing Point3f.

Point3f(float, float, float) - Constructor for class Point3f

Create with values for each dimension.

Point3i - Class in org.anchoranalysis.spatial.point

A three-dimensional point of int values.

Point3i() - Constructor for class Point3i

Creates the points with a 0 in each dimension.

Point3i(int) - Constructor for class Point3i

Create with an identical value in each dimension.

Point3i(int, int, int) - Constructor for class Point3i

Create with values for each dimension.

Point3i(ReadableTuple3i) - Constructor for class Point3i

Creates with the same values as an existing ReadableTuple3i.

PointClamper - Class in org.anchoranalysis.mpp.mark

Ensures a point has values contained inside image-dimensions

PointConverter - Class in org.anchoranalysis.spatial.point

Conversion utilities between points with different types and dimensionalities.

pointIgnoreZ(Point3i) - Method in class BoundingBoxContains

Like BoundingBoxContains.point(ReadableTuple3i) but ignores the z-dimension.

PointList - Class in org.anchoranalysis.mpp.mark.points

PointList() - Constructor for class PointList

PointList(Stream<Point3d>) - Constructor for class PointList

pointListAtFirstPoint(List<Point3i>) - Method in class EncodedVoxels

Sets all points in a list, to point at the first point (the root point) in the list

PointListBase - Class in org.anchoranalysis.mpp.mark.points

PointListBase() - Constructor for class PointListBase

PointListBase(Stream<Point3d>) - Constructor for class PointListBase

PointListFactory - Class in org.anchoranalysis.mpp.mark.points

pointOnContour(Point3d, Orientation) - Method in class FindPointOnContour

pointOnContour(Point3d, Orientation) - Method in class FindPointOnContourWalk

PointRange - Class in org.anchoranalysis.spatial.box

Tracks the range experienced by points in the X, Y and Z dimensions.

PointRange() - Constructor for class PointRange

points() - Method in class MarksInitialization

points() - Method in class ContiguousVoxelPath

The points associated with the path

points() - Method in class LoopablePoints

PointsBean<T> - Class in org.anchoranalysis.mpp.bean.points

PointsBean() - Constructor for class PointsBean

pointsDiscrete() - Method in class Contour

All the points in the contour, converted into Point3i.

PointsFitter - Class in org.anchoranalysis.mpp.bean.points.fitter

PointsFitter() - Constructor for class PointsFitter

PointsFitter - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks

PointsFitter() - Constructor for class PointsFitter

PointsFitterException - Exception in org.anchoranalysis.mpp.bean.points.fitter

PointsFitterException(String) - Constructor for exception PointsFitterException

PointsFitterException(Exception) - Constructor for exception PointsFitterException

PointsFitterToMark - Class in org.anchoranalysis.plugin.points.bean.fitter

PointsFitterToMark() - Constructor for class PointsFitterToMark

PointsFromMask - Class in org.anchoranalysis.image.core.points

Extracts list of points from a Mask.

PointsFromObject - Class in org.anchoranalysis.image.core.points

Derives collections of points from an ObjectMask or its contour.

PointsFromObjects - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection

PointsFromObjects() - Constructor for class PointsFromObjects

PointsFromOrientationProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation

PointsFromOrientationProposer() - Constructor for class PointsFromOrientationProposer

PointsInitialization - Class in org.anchoranalysis.mpp.init

PointsNeighborChecker - Class in org.anchoranalysis.spatial.point

Checks if two or more points fulfill certain neighbor relations to each other.

pointsOnAllOutlines(ObjectCollection) - Static method in class ConvexHullUtilities

pointsOnOutline(ObjectMask) - Static method in class ConvexHullUtilities

PointsProposer - Class in org.anchoranalysis.mpp.bean.proposer

PointsProposer() - Constructor for class PointsProposer

PointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer

Like a IntConsumer but accepts two coordinates of a point as scalar arguments.

Polygon - Class in org.anchoranalysis.mpp.mark.points

Polygon() - Constructor for class Polygon

PolygonCurve - Class in org.anchoranalysis.mpp.mark.points

PolygonCurve() - Constructor for class PolygonCurve

populate(List<NamedBean<FeatureListProvider<FeatureInput>>>, Logger) - Method in class FeatureRelatedInitialization

Populates features into the shared-feature storage from a list of named-beans.

populate(BeanInitializer<?>, Define, Logger) - Method in class ImageInitialization

populate(BeanInitializer<?>, Define, Logger) - Method in class MarksInitialization

populate(BeanInitializer<?>, Define, Logger) - Method in class PointsInitialization

populateFrom(Path) - Method in class HeaderFormat

Creates a ImageMetadata, if possible, from the metadata at path.

populateFrom(Stack, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Method in class MultiBufferSized

populateFromMetadata(Metadata, ImageFileAttributes) - Method in class BMP

populateFromMetadata(Metadata, ImageFileAttributes) - Method in class HeaderFormat

Creates a ImageMetadata, if possible, from metadata.

populateFromMetadata(Metadata, ImageFileAttributes) - Method in class JPEG

populateFromMetadata(Metadata, ImageFileAttributes) - Method in class PNG

populateMissingFromArbitrarySlice(Stack) - Method in class SizeExtents

PopulateStoreFromDefine<V extends BeanInitialization> - Class in org.anchoranalysis.image.bean.nonbean.init

Helps populates a NamedProviderStore from the contents of a Define.

PopulateStoreFromDefine(Define, BeanInitializer<?>, Logger) - Constructor for class PopulateStoreFromDefine

position() - Method in class UnsignedBuffer

The position of the buffer ala Buffer.position.

position(int) - Method in class UnsignedBuffer

Assigns a new position to the buffer.

position(int) - Method in class VoxelBuffer

Assigns a new position to the buffer.

position(int) - Method in class VoxelBufferUnsigned

Position - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single

Position() - Constructor for class Position

PositionProposer - Class in org.anchoranalysis.mpp.bean.proposer

PositionProposer() - Constructor for class PositionProposer

Positive - Annotation Type in org.anchoranalysis.bean.annotation

The bean-field should have a value > 0.

precalculate(ObjectWithProperties, Dimensions) - Method in class BoundingBoxOutline

precalculate(ObjectWithProperties, Dimensions) - Method in class Combine

precalculate(ObjectWithProperties, Dimensions) - Method in class Filled

precalculate(ObjectWithProperties, Dimensions) - Method in class Flatten

precalculate(ObjectWithProperties, Dimensions) - Method in class IfElse

precalculate(ObjectWithProperties, Dimensions) - Method in class Midpoint

precalculate(ObjectWithProperties, Dimensions) - Method in class Nothing

precalculate(ObjectWithProperties, Dimensions) - Method in class Orientation

precalculate(ObjectWithProperties, Dimensions) - Method in class Outline

precalculate(ObjectWithProperties, Dimensions) - Method in class DrawObject

precalculate(ColoredOverlayCollection, DrawOverlay, Dimensions, BinaryValuesByte) - Static method in class DrawOverlay

PrecalculationOverlay - Class in org.anchoranalysis.overlay.writer

Overlays with additional pre-calculations that make them quicker to draw onto a RGBStack

PrecalculationOverlay(ObjectWithProperties) - Constructor for class PrecalculationOverlay

precondition() - Method in class MorphologicalOperatorBase

precondition(ObjectCollection) - Method in class DiscardOutliers

precondition(ObjectCollection) - Method in class GreaterIntersectionWith

precondition(ObjectCollection) - Method in class IntensityGreaterEqualThan

precondition(ObjectCollection) - Method in class IntersectsWith

precondition(ObjectCollection) - Method in class NotTouchingSceneBorder

precondition(ObjectCollection) - Method in class ObjectFilterPredicate

A precondition, which if evaluates to false, cancels the filter i.e.

precondition(ObjectCollection) - Method in class ObjectFilterRelation

PredefinedTasks - Class in org.anchoranalysis.launcher.run.tasks

Loading and printing predefined-tasks.

predicate(Mask) - Method in class IfKeyValueCondition

predicate(Mask) - Method in class IfNotEmpty

predicate(Mask) - Method in class IfObjectFilter

predicate(Mask) - Method in class IfPredicateBase

If this evaluates true, the mask will be returned as-is, otherwise maskElse is returned

predicate(Mask) - Method in class IfStackExists

PredicateAtCorner - Class in org.anchoranalysis.image.voxel.extracter.predicate

Projects a VoxelsPredicate to a corner in a larger global space

PredicateAtCorner(ReadableTuple3i, VoxelsPredicate) - Constructor for class PredicateAtCorner

PredicateBufferBinary<T> - Interface in org.anchoranalysis.image.voxel.iterator.predicate

Like ProcessBufferBinary but returns a boolean.

PredicateImplementation<T> - Class in org.anchoranalysis.image.voxel.extracter.predicate

Implementation of VoxelsPredicate for a particular Voxels.

PredicateImplementation(Voxels<T>, Predicate<T>) - Constructor for class PredicateImplementation

PredicateKernelPointCursor - Interface in org.anchoranalysis.image.voxel.iterator.predicate

Processes a KernelPointCursor and evaluates a predicate on the current position.

PredicateTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.predicate

Like Predicate but takes two bytes as argument.

prefer(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType

Prefer to keep descriptor whose input-class is a sub-class rather than a super-class

prefer(Feature<?>, Feature<?>) - Static method in class FeatureInputType

Like FeatureInputType.prefer(Class, Class) but accepts features directly as input.

prefixPluralize(long, String) - Static method in class LanguageUtilities

Returns n somethings.

prefixPluralizeMaybe(long, String) - Static method in class LanguageUtilities

Returns 1 something or n somethings as is appropriate.

prefixWithDelimeter() - Method in class DirectoryWithPrefix

Prepend - Class in org.anchoranalysis.bean.shared.color.scheme

Prepends a specific color to the list created by another ColorScheme.

Prepend() - Constructor for class Prepend

PrependName - Class in org.anchoranalysis.feature.bean.list

Prepends a string to the custom-name of each feature in a list.

PrependName() - Constructor for class PrependName

PreserveName - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming

Copies files to maintain the same relative-path from the destination file to the destination-directory, as existed from the source file to the source-directory.

PreserveName() - Constructor for class PreserveName

prettyPath(String) - Static method in class PrettyPathConverter

Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user

prettyPath(Path) - Static method in class PrettyPathConverter

Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user

PrettyPathConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert

previousEqualIndex(int) - Method in interface IndexRangeSeek

Finds the previous index in the range before index, or returns index itself if it's a valid index.

previousIndex(int) - Method in interface IndexRangeSeek

Finds the previous index in the range before index.

primaryReport() - Method in class StateReporter

primaryReport() - Method in class StateReporterIdentity

primaryReport() - Method in class StateReporterToPixelized

primaryReport() - Method in class StateReporterTransformer

PrimitiveBeanCollection<T> - Interface in org.anchoranalysis.bean.primitive

A bean that provides a collection of primitive-types or Strings.

PrimitiveConverter - Class in org.anchoranalysis.image.voxel.buffer.primitive

Type conversion between primitive data types.

PrincipalAxisEccentricity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments

Calculates the eccentricity of the Principal Axes (as defined by Image Moments).

PrincipalAxisEccentricity() - Constructor for class PrincipalAxisEccentricity

PrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments

The length of a principal-axis (as defined by Image Moments).

PrincipalAxisLength() - Constructor for class PrincipalAxisLength

PrincipalAxisOrientation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments

An element from orientation of a principal-axis (as defined by Image Moments).

PrincipalAxisOrientation() - Constructor for class PrincipalAxisOrientation

printAllFilesFromTestDirectoryPath(String) - Method in class TestLoader

Prints the names of all files (recursively) in a test-folder to stdout.

printTasksToConsole(Path, Resources, PrintStream) - Static method in class PredefinedTasks

Prints names of the predefined tasks that are available to the application.

PrioritisedVertex - Class in org.anchoranalysis.plugin.image.object.merge.priority

A vertex with a priority attached, and a boolean flag as to whether it can be merged or not

PrioritisedVertex(ObjectMask, double, double, boolean) - Constructor for class PrioritisedVertex

Constructor

Prioritizer - Interface in org.anchoranalysis.plugin.image.object.merge.priority

Creates a priority between two vertices

PriorityQueueIndexRangeDownhill<T> - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding

Implements a priority queue based upon a range of values from 0 to maxValue,

PriorityQueueIndexRangeDownhill(int) - Constructor for class PriorityQueueIndexRangeDownhill

process(Channel, Channel) - Method in class ChannelProviderBinary

process(Channel, Channel, Channel) - Method in class ChannelProviderTernary

process(Point3i, S, T, int, int) - Method in interface ProcessBufferBinary

Processes a voxel location in two buffers.

process(Point3i, VoxelBuffer<S>, T, int, int) - Method in interface ProcessBufferBinaryMixed

Processes a voxel location in two buffers.

process(S, T) - Method in interface ProcessBufferBinaryWithoutOffset

Processes a voxel location in a buffer.

process(Point3i, T, T, T, int, int, int) - Method in interface ProcessBufferTernary

Processes a voxel location in a buffer.

process(Point3i, T, int) - Method in interface ProcessBufferUnary

Processes a voxel location in a buffer.

process(KernelPointCursor) - Method in interface ProcessKernelPointCursor

Processes a particular point.

process(Point3i) - Method in interface ProcessPoint

Processes a particular point.

process(Point3i, int) - Method in interface ProcessPointAndIndex

Processes a particular point.

process(byte, byte) - Method in interface ProcessTwoBytes

Performs the processing.

process(VoxelBuffer<S>, VoxelBuffer<T>, int) - Method in interface ProcessVoxelBufferBinary

Processes a voxel location in a buffer

process(Point3i, VoxelBuffer<S>, T, int) - Method in interface ProcessVoxelBufferBinaryMixed

Processes a voxel location in a buffer

process(VoxelBuffer<S>, VoxelBuffer<T>) - Method in interface ProcessVoxelBufferBinaryWithoutOffset

Processes a voxel location in a buffer

process(VoxelBuffer<T>, int) - Method in interface ProcessVoxelBufferUnary

Processes a voxel location in a buffer.

process(Point3i, VoxelBuffer<T>, int) - Method in interface ProcessVoxelBufferUnaryWithPoint

Processes a voxel location in a buffer.

process(InputBound<MultiInput, S>, DefineOutputter.Processor<ImageInitialization>) - Method in class DefineOutputter

process(T) - Method in interface DefineOutputter.Processor

process(Channel, Channel, Channel) - Method in class MeanThreeChannels

process(Channel, Channel) - Method in class TwoVoxelMappingBase

process(T, EnergyStack) - Method in interface DefineOutputterWithEnergy.ProcessWithEnergyStack

ProcessBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer

Processes a 3D point like ProcessPoint but also retrieves two Buffer for the current z-slice.

ProcessBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer

Processes a 3D point like ProcessPoint but also retrieves both one VoxelBuffer for the current z-slice and one Buffer for the current z-slice.

ProcessBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer

Processes two buffers for each z-slice jointly, without any offset or point.

ProcessBufferTernary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer

Processes a 3D point like ProcessPoint but also retrieves three buffers for the current z-slice.

ProcessBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer

Processes a 3D point like ProcessPoint but also retrieves a buffer for the current z-slice.

ProcessChangedPointAbsoluteMasked<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor

Processes a point which has been translated (changed) relative to another point - and includes global coordinates and includes an object-mask buffer.

processEachSlice(Channel, Consumer<ImageProcessor>) - Static method in class FilterHelper

Applies a Consumer to each slice independently of a Channel.

processEachSlice(BinaryVoxels<UnsignedByteBuffer>, Consumer<ImageProcessor>) - Static method in class FilterHelper

Applies a Consumer to each slice independently of a BinaryVoxels<UnsignedByteBuffer>.

processInput(ExportSharedObjects, InitializationContext, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization, S>) - Method in class DefineOutputterWithEnergy

processInput(InitializationContext, SharedObjects, Optional<Dictionary>, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization, S>) - Method in class DefineOutputterWithEnergy

ProcessKernelPointCursor - Interface in org.anchoranalysis.image.voxel.iterator.process

Processes a KernelPointCursor which includes a Point3i.

processLine(String[], boolean) - Method in interface CSVReaderByLine.ProcessCSVLine

processNeighborhoodPoints(boolean, ProcessVoxelNeighbor<?>) - Method in interface Neighborhood

Calls ProcessVoxelNeighbor for each voxel in the neighborhood of the current state of ProcessVoxelNeighbor.

processPoint(int, int, int, int, int) - Method in interface ProcessChangedPointAbsoluteMasked

Processes a particular point.

processPoint(int, int) - Method in interface ProcessVoxelNeighbor

Processes a particular point.

processPoint(int, int, int, int) - Method in interface ProcessVoxelNeighborAbsolute

Processes a particular point.

ProcessPoint - Interface in org.anchoranalysis.image.voxel.iterator.process

Processes a 3D point.

ProcessPointAndIndex - Interface in org.anchoranalysis.image.voxel.iterator.process

Processes a Point3i also including an index.

processStacks(NamedStacks, Optional<String>, GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase

Processes one set of named-stacks.

processStacks(NamedStacks, Optional<String>, GroupedSharedState<Histogram, Histogram>, InputOutputContext) - Method in class ExportImageHistograms

processStacks(NamedStacks, Optional<String>, GroupedSharedState<Channel, RunningSumChannel>, InputOutputContext) - Method in class GroupedMeanChannelTask

ProcessTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.process

Processes two bytes.

ProcessVoxelBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer

Processes a 3D point like ProcessPoint but also retrieves two VoxelBuffers for the current z-slice.

ProcessVoxelBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer

Processes a 3D point like ProcessVoxelBufferBinary but rather has one VoxelBuffer and one buffer, and also exposes a Point3i.

ProcessVoxelBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer

Processes two voxel-buffers for each z-slice jointly, without any offset or point.

ProcessVoxelBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer

Processes a 3D point like ProcessPoint but also retrieves a VoxelBuffer for the current z-slice.

ProcessVoxelBufferUnaryWithPoint<T,E extends Exception> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer

Processes a 3D point like ProcessVoxelBufferUnary but also exposes a Point3i.

ProcessVoxelNeighbor<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor

Processes a point that is an neighbor of another.

ProcessVoxelNeighborAbsolute<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor

Processes a point that is a neighbor of another - includes global (absolute) coordinates for this point.

ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor

Like ProcessVoxelNeighborAbsolute but additionally includes a SlidingBuffer.

ProcessVoxelNeighborAbsoluteWithSlidingBuffer(SlidingBuffer<?>) - Constructor for class ProcessVoxelNeighborAbsoluteWithSlidingBuffer

Creates for a particular sliding buffer.

ProcessVoxelNeighborFactory - Class in org.anchoranalysis.image.voxel.iterator.neighbor

Creates ProcessVoxelNeighbor to match certain circumstances.

Progress - Interface in org.anchoranalysis.core.progress

Tracks the completion of an operation, as divided into sub-units of progress.

ProgressConsole - Class in org.anchoranalysis.core.progress

Displays the current progress on the console.

ProgressConsole(int) - Constructor for class ProgressConsole

ProgressIgnore - Class in org.anchoranalysis.core.progress

Placeholder that doesn't measure any progress.

ProgressIncrement - Class in org.anchoranalysis.core.progress

Like Progress but rather than explicitly setting a value for progress, the value increments with the ProgressIncrement.update() operation.

ProgressIncrement(Progress) - Constructor for class ProgressIncrement

progressing() - Method in interface CheckedSupplier

An interface to a similar supplier that monitors progress.

ProgressMultiple - Class in org.anchoranalysis.core.progress

Exposes several underlying child Progress trackers as a unitary parent tracker.

ProgressMultiple(Progress, int) - Constructor for class ProgressMultiple

Creates for a particular number of child trackers.

ProjectableBuffer<T> - Interface in org.anchoranalysis.image.voxel.buffer

A buffer to which slices may be added to form a projection.

projectMax() - Method in class Channel

A maximum-intensity projection across the z-slices.

projectMax() - Method in class DisplayStack

Creates a Maximum Intensity Projection of each channel.

projectMax() - Method in class Stack

Creates a Maximum Intensity Projection of each channel.

projectMax() - Method in class StackNotUniformSized

Creates a Maximum Intensity Projection of each channel.

projectMax() - Method in class BoundedVoxels

A maximum-intensity projection (flattens in z dimension)

projectMax() - Method in interface VoxelsExtracter

A maximum intensity projection of all slices

projectMean() - Method in class Channel

A mean-intensity projection across the z-slices.

projectMean() - Method in interface VoxelsExtracter

A mean intensity projection of all slices.

propertyValues() - Method in class PermuteProperty

An iterator with possible alternative values for the property.

propertyValues() - Method in class PermutePropertyDoubleSet

propertyValues() - Method in class PermutePropertySequenceDouble

propertyValues() - Method in class PermutePropertySequenceInteger

propertyValues() - Method in class PermutePropertyStringSet

ProposalAbnormalFailureException - Exception in org.anchoranalysis.mpp.proposer

An exception when a proposal could not be made for an abnormal reason

ProposalAbnormalFailureException(String, Throwable) - Constructor for exception ProposalAbnormalFailureException

ProposalAbnormalFailureException(String) - Constructor for exception ProposalAbnormalFailureException

ProposalAbnormalFailureException(Throwable) - Constructor for exception ProposalAbnormalFailureException

propose(MarkWithIdentifierFactory, ProposerContext) - Method in class MarkCollectionProposer

propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class MarkMergeProposer

propose(VoxelizedMarkMemo, ProposerContext) - Method in class MarkProposer

propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class MarkSplitProposer

propose(Mark, Dimensions, RandomNumberGenerator) - Method in class OrientationProposer

propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class PointsProposer

propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class RadiiProposer

propose(RandomNumberGenerator, Optional<Resolution>) - Method in class ScalarProposer

propose(ProposerContext) - Method in interface OptionalPointProposer

propose(MarkWithIdentifierFactory, ProposerContext) - Method in class CreateNew

propose(MarkWithIdentifierFactory, ProposerContext) - Method in class FromMarkProposer

propose(MarkWithIdentifierFactory, ProposerContext) - Method in class FromObjects

propose(MarkWithIdentifierFactory, ProposerContext) - Method in class FromProvider

propose(MarkWithIdentifierFactory, ProposerContext) - Method in class FromSerializedMarks

propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class Check

propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class ChooseOneList

propose(VoxelizedMarkMemo, ProposerContext) - Method in class FromSerializedObject

propose(VoxelizedMarkMemo, ProposerContext) - Method in class MarkProposerFromList

propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class MarkProposerFromList

propose(VoxelizedMarkMemo, ProposerContext) - Method in class MarkProposerReference

propose(VoxelizedMarkMemo, ProposerContext) - Method in class MarkProposerUnary

propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class MarkProposerUnary

propose(VoxelizedMarkMemo, ProposerContext) - Method in class ObjectAsPoints

propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class OrderedList

propose(VoxelizedMarkMemo, ProposerContext) - Method in class OrientationAndRadiiProposer

propose(VoxelizedMarkMemo, ProposerContext) - Method in class Position

propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class Repeat

propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class MarkMergeProposerReference

propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class MergeMarkEllipse

propose(Mark, Dimensions, RandomNumberGenerator) - Method in class RandomOrientation

propose(Mark, Dimensions, RandomNumberGenerator) - Method in class RandomXY

propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class IncludeRandomObjects

propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class XYOrientationExtendToZ

propose(ProposerContext) - Method in class Repeat

propose(ProposerContext) - Method in class UniformRandom

propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class RadiiProposerRepeat

propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class UniformRandomRadiiProposer

propose(RandomNumberGenerator, Optional<Resolution>) - Method in class Constant

propose(RandomNumberGenerator, Optional<Resolution>) - Method in class FromUnitValueDistance

propose(RandomNumberGenerator, Optional<Resolution>) - Method in class GaussianSampler

propose(RandomNumberGenerator, Optional<Resolution>) - Method in class MaxWithConstant

propose(RandomNumberGenerator, Optional<Resolution>) - Method in class Scale

propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class MarkSplitProposerReference

propose(VoxelizedMarkMemo, ProposerContext) - Method in class FitPoints

proposeKernel(RandomNumberGenerator) - Method in class KernelProposer

proposeNewMarks(MarksFromPartition, int, KernelCalculationContext) - Method in class KernelBirthPartition

proposeNewMarks(T, int, KernelCalculationContext) - Method in class KernelBirth

proposeNewMarks(VoxelizedMarksWithEnergy, int, KernelCalculationContext) - Method in class KernelBirthVoxelized

proposer() - Method in class KernelCalculationContext

ProposerBean<T> - Class in org.anchoranalysis.mpp.bean.proposer

ProposerBean() - Constructor for class ProposerBean

ProposerContext - Class in org.anchoranalysis.mpp.proposer

ProposerContext(RandomNumberGenerator, EnergyStack, RegionMap, ErrorNode) - Constructor for class ProposerContext

ProposerException - Exception in org.anchoranalysis.mpp.proposer

An exception thrown when something goes wrong in a Proposer

ProposerException(String) - Constructor for exception ProposerException

ProposerException(Throwable) - Constructor for exception ProposerException

ProposerFailureDescription - Class in org.anchoranalysis.mpp.proposer.error

ProposerFailureDescription() - Constructor for class ProposerFailureDescription

Provider<T> - Interface in org.anchoranalysis.bean

A class (usually an AnchorBean) that creates or otherwise supplies another object.

ProviderAsStack - Interface in org.anchoranalysis.image.core.stack

Provides a stack-representation of an entity.

ProvidesStackInput - Interface in org.anchoranalysis.image.io.stack.input

Base class for inputs which somehow eventually send up providing stacks, with or without names.

ProvisionFailedException - Exception in org.anchoranalysis.bean.xml.exception

If provisioning an object fails.

ProvisionFailedException(String) - Constructor for exception ProvisionFailedException

Creates with only a message.

ProvisionFailedException(Throwable) - Constructor for exception ProvisionFailedException

Creates with only a cause.

ProvisionFailedException(String, Throwable) - Constructor for exception ProvisionFailedException

Creates with both a message and cause.

put(K, V) - Method in class LRUCache

Puts a key-value pair irrespective of whether its already present or not.

put(String, String) - Method in class Dictionary

Inserts a key-value pair.

put(String, double) - Method in class Dictionary

Inserts a key-value pair, after converting value to a String.

put(U, S) - Method in class CalculationPartMap

Assigns a evaluation result to the cache for a particular key.

put(ByteBuffer) - Method in class UnsignedByteBuffer

Relative put-method from an unsigned byte buffer, represented by a ByteBuffer.

put(UnsignedByteBuffer) - Method in class UnsignedByteBuffer

Relative put-method from an unsigned byte buffer, represented by a UnsignedByteBuffer.

put(ShortBuffer) - Method in class UnsignedShortBuffer

Relative put-method from an unsigned short buffer, represented by a ShortBuffer.

put(UnsignedShortBuffer) - Method in class UnsignedShortBuffer

Relative put-method from an unsigned short buffer, represented by a UnsignedShortBuffer.

put(T, int) - Method in class PriorityQueueIndexRangeDownhill

put(String, CSVRow) - Method in class MapGroupToRow

putByte(int, byte) - Method in class VoxelBuffer

Puts a byte in the buffer at a particular position, converting, if necessary, to the buffer type.

putCheck(String, String) - Method in class Dictionary

Inserts a key/value pair, checking that the key doesn't already exist.

putCheck(String, double) - Method in class Dictionary

Inserts a key/value pair, checking that the key doesn't already exist.

putCheck(Dictionary) - Method in class Dictionary

Inserts all key/value pairs from another dictionary, checking that no key already exists.

putCode(int, int) - Method in class EncodedIntBuffer

putDouble(double) - Method in class UnsignedBuffer

Puts a double at the current buffer position.

putDouble(int, double) - Method in class UnsignedBuffer

Puts a double at a particular buffer position.

putDouble(double) - Method in class UnsignedByteBuffer

putDouble(int, double) - Method in class UnsignedByteBuffer

putDouble(double) - Method in class UnsignedIntBuffer

putDouble(int, double) - Method in class UnsignedIntBuffer

putDouble(double) - Method in class UnsignedShortBuffer

putDouble(int, double) - Method in class UnsignedShortBuffer

putDoubleClamped(double) - Method in class UnsignedByteBuffer

Puts a double at the current buffer position, clamping to ensure the value is within the range (0,255).

putFloat(float) - Method in class UnsignedBuffer

Puts a float at the current buffer position.

putFloat(int, float) - Method in class UnsignedBuffer

Puts a float at a particular buffer position.

putFloat(float) - Method in class UnsignedByteBuffer

putFloat(int, float) - Method in class UnsignedByteBuffer

putFloat(float) - Method in class UnsignedIntBuffer

putFloat(int, float) - Method in class UnsignedIntBuffer

putFloat(float) - Method in class UnsignedShortBuffer

putFloat(int, float) - Method in class UnsignedShortBuffer

putFloatClamped(float) - Method in class UnsignedByteBuffer

Puts a float at the current buffer position, clamping to ensure the value is within the range (0,255).

putFloatClamped(float) - Method in class UnsignedShortBuffer

Puts a float at the current buffer position, clamping to ensure the value is within the range (0,255).

putInstanceFor(Class<? extends T>, T) - Method in class BeanInstanceMap

Assigns an instance to a particular family-type.

putInt(int, int) - Method in class VoxelBuffer

Puts a int in the buffer at a particular position, converting, if necessary, to the buffer type.

putInt(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer

Assign a value to the buffer at a particular absolute position.

putLong(long) - Method in class UnsignedBuffer

Puts a long at the current buffer position.

putLong(long) - Method in class UnsignedByteBuffer

putLong(long) - Method in class UnsignedIntBuffer

putLong(long) - Method in class UnsignedShortBuffer

putLongClamped(long) - Method in class UnsignedShortBuffer

Puts a long at the current buffer position, clamping to ensure the value is within the range (0,255).

putRaw(byte) - Method in class UnsignedByteBuffer

Puts an unsigned-byte (represented as a byte) at the current buffer position.

putRaw(int, byte) - Method in class UnsignedByteBuffer

Puts an unsigned-byte (represented as a byte) a particular buffer position.

putRaw(int) - Method in class UnsignedIntBuffer

Puts an unsigned-int (represented as a int) at the current buffer position.

putRaw(int, int) - Method in class UnsignedIntBuffer

Puts an unsigned-int (represented as a int) a particular buffer position.

putRaw(short) - Method in class UnsignedShortBuffer

Puts an unsigned-short (represented as a short) at the current buffer position.

putRaw(int, short) - Method in class UnsignedShortBuffer

Puts an unsigned-short (represented as a short) a particular buffer position.

putUnsigned(int) - Method in class UnsignedBufferAsInt

Puts an unsigned-byte (represented by an int) at current buffer position.

putUnsigned(int, int) - Method in class UnsignedBufferAsInt

Puts an unsigned-byte (represented as a int) a particular buffer position.

putUnsigned(int) - Method in class UnsignedByteBuffer

putUnsigned(int, int) - Method in class UnsignedByteBuffer

putUnsigned(long) - Method in class UnsignedIntBuffer

Puts an unsigned-int (represented by a long) at current buffer position.

putUnsigned(int, long) - Method in class UnsignedIntBuffer

Puts an unsigned-int (represented as a long) a particular buffer position.

putUnsigned(int) - Method in class UnsignedShortBuffer

putUnsigned(int, int) - Method in class UnsignedShortBuffer

putUnsignedClamped(int) - Method in class UnsignedShortBuffer

Puts a long at the current buffer position, clamping to ensure the value is within the range (0,255).

putUnsignedInt(int) - Method in class UnsignedByteBuffer

Puts an unsigned-int (represented by a int) at current buffer position.

PxlListOperationFromMark - Class in org.anchoranalysis.mpp.feature.bean.mark

PxlListOperationFromMark() - Constructor for class PxlListOperationFromMark

PxlMarkMemoFactory - Class in org.anchoranalysis.mpp.mark.voxelized.memo

Q

QuadraticEquationSolver - Class in org.anchoranalysis.math.equation

Solves a Quadratic Equation by finding non-complex roots.

QuadraticEquationSolver.QuadraticRoots - Class in org.anchoranalysis.math.equation

Roots (solution) of a quadratic equation.

QuadraticRoots(double, double) - Constructor for class QuadraticEquationSolver.QuadraticRoots

Quantile - Class in org.anchoranalysis.feature.bean.results

The quantile of the results from a particular feature.

Quantile() - Constructor for class Quantile

quantile(double) - Method in interface VoxelStatistics

The voxel value corresponding to a particular quantile.

quantile(double) - Method in class VoxelStatisticsCombined

quantile(double) - Method in class VoxelStatisticsFromHistogram

quantile(double) - Method in class Histogram

Calculates the corresponding value for a particular quantile in the distribution of values in the histogram.

Quantile - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold

Calculates the threshold value from a quantile of a histogram.

Quantile() - Constructor for class Quantile

Quantile - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

Quantile() - Constructor for class Quantile

QuantileAcrossConnectedComponents - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object

Calculates the median of a feature applied to each connected component

QuantileAcrossConnectedComponents() - Constructor for class QuantileAcrossConnectedComponents

QuantileAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object

Calculates the quantile of a feature applied to each connected component

QuantileAcrossObjects() - Constructor for class QuantileAcrossObjects

QuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel

Converts a Channel to UnsignedByteBuffer by scaling against a quantile of the intensity values that appear in it.

QuantileIntensity(double) - Constructor for class QuantileIntensity

Scales against a particular quantile of the intensity values.

QuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram

Converts a Channel to UnsignedByteBuffer by scaling against a quantile of the intensity values from a corresponding histogram.

QuantileIntensityFromHistogram(double) - Constructor for class QuantileIntensityFromHistogram

Scales against a particular quantile of the intensity values.

QuantileStretch - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity

Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range

QuantileStretch() - Constructor for class QuantileStretch

QuickBase<T extends InputFromManager> - Class in org.anchoranalysis.plugin.quick.bean.input

A base for quick managers that make various assumptions about file-structure.

QuickBase() - Constructor for class QuickBase

QuickExperiment<S> - Class in org.anchoranalysis.plugin.quick.bean.experiment

A quick way of defining an InputOutputExperiment where several assumptions are made.

QuickExperiment() - Constructor for class QuickExperiment

QuickMultiDatasetExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.quick.bean.experiment

Makes a lot of assumptions, that allows us to reduce the number of inputs to an InputOutputExperiment.

QuickMultiDatasetExperiment() - Constructor for class QuickMultiDatasetExperiment

QuickMultiDatasetStructuredExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.quick.bean.structure

Similar to QuickMultiDatasetStructuredExperiment put sets properties according to an expected directory structure.

QuickMultiDatasetStructuredExperiment() - Constructor for class QuickMultiDatasetStructuredExperiment

quickOverlap() - Method in class Ellipse

quickOverlap() - Method in class Ellipsoid

quickOverlap() - Method in class MarkWithPositionAndSingleRadius

quickOverlap() - Method in class Mark

An alternative "quick" metric for overlap for a Mark.

QuickOverlapCalculation - Interface in org.anchoranalysis.mpp.mark

A method to quickly calculate overlap approximately

R

RadiiMinRatio - Class in org.anchoranalysis.plugin.mpp.bean.check

RadiiMinRatio() - Constructor for class RadiiMinRatio

radiiOrdered() - Method in class ConicBase

radiiOrderedResolved(Optional<Resolution>) - Method in class ConicBase

RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer

RadiiProposer() - Constructor for class RadiiProposer

RadiiProposerRepeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii

RadiiProposerRepeat() - Constructor for class RadiiProposerRepeat

RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic

Utility functions for generating random radii for ConicBase

RadiiRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii

RadiiRatio() - Constructor for class RadiiRatio

radiusForRegion(int) - Method in class MarkWithPositionAndSingleRadius

radiusForRegionSquared(int) - Method in class MarkWithPositionAndSingleRadius

RandomCollection<T> - Class in org.anchoranalysis.mpp.pair

A collection of items from which one can randomly sample

RandomCollection() - Constructor for class RandomCollection

RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria

An implementation of a RandomCollection that uses AddCriteria

RandomCollectionWithAddCriteria(Class<?>) - Constructor for class RandomCollectionWithAddCriteria

randomIndex(RandomNumberGenerator) - Method in class MarkCollection

randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class RadiiRandomizer

randomMark(RandomNumberGenerator) - Method in class MarkCollection

RandomNumberGenerator - Interface in org.anchoranalysis.core.random

Generates random numbers from various distributions.

RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random

A bean that defines a type of RandomNumberGenerator.

RandomNumberGeneratorBean() - Constructor for class RandomNumberGeneratorBean

RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random

Implements a random-number generator using the MersenneTwister algorithm.

RandomNumberGeneratorMersenne(boolean) - Constructor for class RandomNumberGeneratorMersenne

Creates indicating whether to use a fixed-seed or not.

RandomOrder - Class in org.anchoranalysis.plugin.io.bean.file.provider

RandomOrder() - Constructor for class RandomOrder

randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation

randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation2D

randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation3D

RandomOrientation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation

RandomOrientation() - Constructor for class RandomOrientation

RandomOrientation(BoundRotation) - Constructor for class RandomOrientation

RandomXY - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation

RandomXY() - Constructor for class RandomXY

randOpen(RandomNumberGenerator) - Method in class ResolvedBound

A random value between the bounds (open interval)

Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

The range (difference in values) between two quantiles

Range() - Constructor for class Range

Range<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range

The statistical range between two values i.e.

Range() - Constructor for class Range

rangeChannelNum() - Method in class ParsedFilePathBag

RangeCompareBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range

RangeCompareBase() - Constructor for class RangeCompareBase

RangeCompareFromScalars<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range

A base-class for setting the boundaries of the range using constant scalars

RangeCompareFromScalars() - Constructor for class RangeCompareFromScalars

rangeCPresent() - Method in class SizeExtents

rangeLimitsIfEmpty(DefaultCategoryDataset) - Method in class BarPlot

rangeLimitsIfEmpty(DefaultBoxAndWhiskerCategoryDataset) - Method in class BoxPlot

rangeLimitsIfEmpty(XYDataset) - Method in class LinePlot

rangeLimitsIfEmpty(S) - Method in class PlotIndexBase

rangeSliceNum() - Method in class ParsedFilePathBag

rangeTimeIndex() - Method in class ParsedFilePathBag

rangeTPresent() - Method in class SizeExtents

RasterArranger - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange

RasterArranger() - Constructor for class RasterArranger

RasterDirectoryObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.mask

Writes each object as a binary Mask in a directory.

RasterGenerator<T> - Class in org.anchoranalysis.image.io.stack.output.generator

Transfroms an entity to a Stack and writes it to the file-system.

RasterGenerator() - Constructor for class RasterGenerator

RasterGeneratorBridge<T,V> - Class in org.anchoranalysis.image.io.stack.output.generator

Allows us to call an RasterGenerator<S> as if it was an RasterGenerator<T> using an function to connect the two.

RasterGeneratorBridge(RasterGenerator<V>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class RasterGeneratorBridge

RasterGeneratorDelegateToDisplayStack<T> - Class in org.anchoranalysis.image.io.stack.output.generator

Delegates a RasterGeneratorSelectFormat to a SingleFileTypeGenerator<T, DisplayStack>.

RasterGeneratorDelegateToDisplayStack(SingleFileTypeGenerator<T, DisplayStack>, boolean) - Constructor for class RasterGeneratorDelegateToDisplayStack

RasterGeneratorDelegateToRaster<S,T> - Class in org.anchoranalysis.image.io.stack.output.generator

Uses a delegate raster-generator and optionally applies a conversions before calling RasterGeneratorDelegateToRaster.transform(T).

RasterGeneratorDelegateToRaster(RasterGenerator<S>) - Constructor for class RasterGeneratorDelegateToRaster

RasterGeneratorSelectFormat<T> - Class in org.anchoranalysis.image.io.stack.output.generator

A RasterGenerator that selects an appropriate output-format based upon each generated image.

RasterGeneratorSelectFormat() - Constructor for class RasterGeneratorSelectFormat

rasterResizing() - Method in class InterpolatorFactory

An Interpolator that is suitable for resizing a raster-image with a range of intensity values.

RasterTask<S,U> - Class in org.anchoranalysis.plugin.image.task.bean

An experiment that takes (primarily) a series of raster images as an input.

RasterTask() - Constructor for class RasterTask

RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair

Ratio of first-object to second-object in a pair.

RatioFirstToSecond() - Constructor for class RatioFirstToSecond

RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

RatioNonMode() - Constructor for class RatioNonMode

RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments

Calculates the ratio of prinicpal-axis length using Image Moments.

RatioPrincipalAxisLength() - Constructor for class RatioPrincipalAxisLength

RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold

RatioThreshold() - Constructor for class RatioThreshold

read(Path, Logger) - Method in interface AnnotationReader

Reads an annotation, if possible, from the file-system.

read(Path, Logger) - Method in class ImageLabelAnnotationReader

read(Path, Logger) - Method in class DualMarksAnnotationReader

read(Path) - Method in class CSVReader

Opens a CSV for reading.

read(CSVReaderByLine.ProcessCSVLine) - Method in class ReadByLine

Reads a CSV-file iterating through each row and passing it to lineProcessor

ReadableTuple3i - Interface in org.anchoranalysis.spatial.point

A tuple with three-values, respectively for the X, Y and Z dimensions.

readAcquisitionDate(Path) - Static method in class AcquisitionDateReader

Reads an image acquisition-date from a file identified by path, based on the present of EXIF data.

readAcquisitionDate(Metadata) - Static method in class AcquisitionDateReader

Reads an image acquisition-date from metadata, based on the present of EXIF data.

ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy

readAssumeExists(Path, Logger) - Static method in class ReadAnnotationFromFile

ReadByLine - Class in org.anchoranalysis.io.input.csv

ReadByLine(Path, CSVReader) - Constructor for class ReadByLine

readCheckExists(Path, Logger) - Static method in class ReadAnnotationFromFile

readDate(Metadata, Class<T>, int[], int[]) - Static method in class ReadMetadataUtilities

Reads a metadata entry of type Date from the first directory of type directoryType.

readDate(Directory, int) - Static method in class ReadMetadataUtilities

Reads a metadata entry of type Date from a Directory.

readDefaultMarks(Path, Logger) - Method in class DualMarksAnnotationReader

Reads the annotations as a MarkCollection from the file-system.

readFileAsString(Path) - Static method in class TextFileReader

Reads all the lines in a text-file into a string.

readFromCSV(Path, boolean) - Static method in class FileLabelMap

readFromFile(Path) - Static method in class Dictionary

Reads parameters from a Java properties file.

ReadFromFile - Class in org.anchoranalysis.io.input.bean.dictionary

Reads a Dictionary from a file in Java properties format.

ReadFromFile() - Constructor for class ReadFromFile

readFromWidthHeightTags(Metadata, Class<T>, int, int) - Static method in class ReadMetadataUtilities

Reads two metadata entries, representing width and height, and use them to form a Extent.

readFromWidthHeightTags(Directory, int, int) - Static method in class ReadMetadataUtilities

Reads two metadata entries, representing width and height, and use them to form a Extent.

readHistogramFromFile(Path) - Static method in class HistogramCSVReader

readInt(Metadata, Class<T>, int) - Static method in class ReadMetadataUtilities

Reads a metadata entry of type int from the first directory of type directoryType.

readInt(Directory, int) - Static method in class ReadMetadataUtilities

Reads a metadata entry of type int from a Directory.

readLine() - Method in class CSVReader.OpenedCSVFile

readLinesAsList(Path) - Static method in class TextFileReader

Reads all the lines in a text-file into a list of strings.

readMetadata(Path) - Static method in class ReadMetadataUtilities

Reads metadata, if it exists, from an image.

readMetadata(Path, boolean) - Static method in class ReadVoxelExtentXml

Looks for a metadata file describing the resolution

ReadMetadataUtilities - Class in org.anchoranalysis.io.bioformats.metadata

Reads various image properties from tags in Metadata.

ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options

Options that influence how stack is read in BioformatsReader.

ReadOptions() - Constructor for class ReadOptions

ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options

Forces a particular settings, but otherwise uses settings from a delegate

ReadOptionsDelegate() - Constructor for class ReadOptionsDelegate

readResolutionXml(File) - Static method in class ResolutionAsXml

Retrieves resolution from a XML file previously written by ResolutionAsXml.writeResolutionXml(Resolution, Path).

readStack(Path, Logger) - Method in class StackReader

Opens a file at path that should contain only a single-stack.

ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader

Reads Resolution from an XML file associated an image.

ReadVoxelExtentXml() - Constructor for class ReadVoxelExtentXml

reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstruction2DIJ

reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstructionByErosion

reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstructionRobinson

recordCopiedOutput(Path, Optional<Path>, int) - Method in class RecordingCounter

Records an copy operation in the log / CSV path mapping.

RecordedExecutionTimes - Class in org.anchoranalysis.core.time

Recorded execution-times for operations.

RecordedExecutionTimes(Stream<RecordedExecutionTimes.RecordedOperation>) - Constructor for class RecordedExecutionTimes

Create with the running-times.

RecordedExecutionTimes.RecordedOperation - Class in org.anchoranalysis.core.time

A particular type of operation that has been recorded (en aggregate).

RecordedOperation(String, int, double, double, int) - Constructor for class RecordedExecutionTimes.RecordedOperation

RecordedOutputs - Class in org.anchoranalysis.io.output.recorded

Outputs recorded from RecordOutputNamesForWriter.

RecordedOutputs() - Constructor for class RecordedOutputs

recordedOutputs() - Method in class RecordingWriters

If defined, all output-names that are passed as arguments to both writers are recorded here.

RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded

Rules to determine what outputting occurs, together with maybe an entity that records the output-names that are used when writing / querying.

RecordedOutputsWithRules() - Constructor for class RecordedOutputsWithRules

Creates with no rules or outputs defined.

RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class RecordedOutputsWithRules

Creates with all elements defined.

recordedTimes() - Method in class ExecutionTimeRecorder

The execution-times that have been recorded.

recordedTimes() - Method in class ExecutionTimeRecorderIgnore

recordError(Class<?>, String, Throwable) - Method in interface ErrorReporter

Reports an error that occurred as an exception, with a message first introducing it.

recordError(Class<?>, Throwable) - Method in interface ErrorReporter

Reports an error that occurred as an exception

recordError(Class<?>, String) - Method in interface ErrorReporter

Reports an error with a constant string error message.

recordError(Class<?>, Throwable) - Method in class ErrorReporterBase

recordError(Class<?>, String) - Method in class ErrorReporterBase

recordError(Class<?>, String, Throwable) - Method in class ErrorReporterBase

recordError(Class<?>, Throwable) - Method in class ErrorReporterForTask

recordError(Class<?>, String) - Method in class ErrorReporterForTask

recordError(Class<?>, String, Throwable) - Method in class ErrorReporterForTask

recordErrorFormatted(Class<?>, String, Object...) - Method in interface ErrorReporter

Reports an error with a string derived from a format-string.

recordExecutionTime(String, long) - Method in class ExecutionTimeRecorder

Records the execution-time of a particular operation.

recordExecutionTime(String, CheckedRunnable<E>) - Method in class ExecutionTimeRecorder

Executes an operation while recording the execution-time - with a return type.

recordExecutionTime(String, CheckedSupplier<T, E>) - Method in class ExecutionTimeRecorder

Executes an operation while recording the execution-time - with a return type.

recordExecutionTime(String, long) - Method in class ExecutionTimeRecorderIgnore

RecordingCounter<T> - Class in org.anchoranalysis.plugin.io.shared

A counter that also records a manifest of copied outputs in a message-log and CSV file.

RecordingCounter(Counter, Outputter, T) - Constructor for class RecordingCounter

RecordingWriters - Class in org.anchoranalysis.io.output.recorded

Two writers that record any output-names that are passed as arguments.

RecordingWriters(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class RecordingWriters

Creates the two writers.

recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class MutableDirectory

recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class DualWriterOperationRecorder

recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in interface WriteOperationRecorder

Records a subdirectory that has been recated.

recordTimeDifferenceBetween(String, long, long) - Method in class ExecutionTimeRecorder

Records the execution-time of a particular operation by subtracting the start-time from the end time.

recordWarning(String) - Method in interface ErrorReporter

Reports an warning with a constant string error message.

recordWarning(String) - Method in class ErrorReporterBase

recordWarning(String) - Method in class ErrorReporterForTask

recordWarningFormatted(String, Object...) - Method in interface ErrorReporter

Reports an warning with a string derived from a format-string.

recordWrittenFile(String, ManifestDescription, Path, String) - Method in class JobRootDirectory

recordWrittenFile(String, ManifestDescription, Path, String) - Method in class RootDirectory

recordWrittenFile(String, ManifestDescription, Path, String) - Method in class Subdirectory

recordWrittenFile(String, ManifestDescription, Path, String) - Method in class DualWriterOperationRecorder

recordWrittenFile(String, ManifestDescription, Path, String) - Method in interface WriteOperationRecorder

Records a file written.

RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly

Generates a nice string representation of an Exception and its causes according to certain rules.

RED - Static variable in class RGBChannelNames

Name for the red channel.

red() - Method in class RGBStack

The red channel.

reduce() - Method in class HungarianAlgorithm

Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.

reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class ThresholdConfidence

ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair

Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.

ReduceFirstAndSecond() - Constructor for class ReduceFirstAndSecond

ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair

Calculates the aggregate of the ratio of first:second and second:first for a FeatureInputPairObjects

ReduceRatioFirstAndSecond() - Constructor for class ReduceRatioFirstAndSecond

Reference<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator

Uses another feature to calculate the value.

Reference(String) - Constructor for class Reference

Create with a specific identifier.

Reference() - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider

Reference(String) - Constructor for class Reference

Reference() - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider

Reference(String) - Constructor for class Reference

Reference() - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider

Reference(String) - Constructor for class Reference

Reference() - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider

Reference(String) - Constructor for class Reference

Reference() - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider

Retrieves an existing stack.

Reference(String) - Constructor for class Reference

Reference() - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection

Reference() - Constructor for class Reference

Reference(String) - Constructor for class Reference

Reference - Class in org.anchoranalysis.plugin.points.bean.fitter

Reference() - Constructor for class Reference

ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider

Creates reference (i.e.

ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider

Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.

ReferenceOrElse() - Constructor for class ReferenceOrElse

ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection

Returns an existing marks-collection or an empty set if it doesn't exist

ReferenceOrEmpty() - Constructor for class ReferenceOrEmpty

ReferencingFeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list

A base class for implementations of FeatureListProvider that may reference features created elsewhere.

ReferencingFeatureListProvider() - Constructor for class ReferencingFeatureListProvider

ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter

Reflects points in each axes if all points are within a certain distance from it

ReflectInAxesWithinDistance() - Constructor for class ReflectInAxesWithinDistance

reflectThroughOrigin() - Method in class BoundingBox

Reflects the bounding box through the origin.

RegEx - Class in org.anchoranalysis.bean.shared.regex

The regular-expression to use for matching groups.

RegEx() - Constructor for class RegEx

RegExList - Class in org.anchoranalysis.bean.shared.regex

Combines one or more RegEx together, by successively trying to match each RegEx until success.

RegExList() - Constructor for class RegExList

RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.file.namer

RegExMatcher() - Constructor for class RegExMatcher

RegExSimple - Class in org.anchoranalysis.bean.shared.regex

Matches a Java-style regular expression against the string.

RegExSimple(String) - Constructor for class RegExSimple

Creates with an expression that should match one or more groups.

RegExSimple() - Constructor for class RegExSimple

RegExSimple(String, Pattern) - Constructor for class RegExSimple

region() - Method in interface AnnotationWithMarks

The region(s) of the marks that specifies the annotation.

region() - Method in class DualMarksAnnotation

region(BoundingBox, boolean) - Method in class Mask

Creates an ObjectMask corresponding to the on/off state in a bounding-box.

region(BoundingBox, boolean) - Method in class BoundedVoxels

A (sub-)region of the voxels.

region(BoundingBox, boolean) - Method in interface VoxelsExtracter

A (sub-)region of the voxels.

region(BoundingBox, boolean) - Method in class ObjectMask

A (sub-)region of the object-mask.

regionIntersecting(BoundingBox, int) - Method in class BoundedVoxels

Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.

regionIntersecting(BoundingBox) - Method in class ObjectMask

Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)

RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap

Maps integer IDs to sub-regions in the map

RegionMap(int) - Constructor for class RegionMap

RegionMap() - Constructor for class RegionMap

RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap

RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap

RegionMembership(int) - Constructor for class RegionMembership

RegionMembership() - Constructor for class RegionMembership

RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap

RegionMembershipAnd() - Constructor for class RegionMembershipAnd

RegionMembershipAnd(int) - Constructor for class RegionMembershipAnd

RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap

RegionMembershipOr() - Constructor for class RegionMembershipOr

RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap

RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap

RegionMembershipWithFlags(RegionMembership, int) - Constructor for class RegionMembershipWithFlags

regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels

Creates an box with a subrange of the slices.

regionZ(int, int) - Method in class ObjectMask

Creates an object-mask with a subrange of the slices.

register(String, AnchorBeanFactory) - Static method in class RegisterBeanFactories

Registers a specific factory.

register(String, Function<List<T>, Object>) - Static method in class RegisterBeanFactories

Registers a bean that creates a {link java.util.List}.

registerAllPackageBeanFactories() - Static method in class RegisterBeanFactories

Registers the factories for the beans that exist in this package

RegisterBeanFactories - Class in org.anchoranalysis.bean.xml

Utility class for registering the Bean-factories that are found in anchor-bean (or any other).

registerBeanFactories() - Static method in class RegisterBeanFactoriesImage

RegisterBeanFactoriesImage - Class in org.anchoranalysis.image.bean

Registers beans that needs particular factories

RegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.group.parser

RegularExpression() - Constructor for class RegularExpression

RegularExpressionBase - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming

A base class for CopyFilesNaming classes that use a regular-expression.

RegularExpressionBase() - Constructor for class RegularExpressionBase

rejected() - Method in interface DualMarks

The rejected marks.

RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader

If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.

RejectIfConditionXYResolution() - Constructor for class RejectIfConditionXYResolution

RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score

RejectIfIntensityLessThan() - Constructor for class RejectIfIntensityLessThan

RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected

Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)

RejectIfNotConnected() - Constructor for class RejectIfNotConnected

rejectProposal() - Method in class OptimizationStep

relation() - Method in class RelationToConstant

relation() - Method in class RelationToThreshold

The relation to the threshold.

relation() - Method in class BinaryNotOffVoxels

relation() - Method in class BinaryNotOnVoxels

relation() - Method in class BinaryOffVoxels

relation() - Method in class BinaryOnVoxels

RelationBean - Class in org.anchoranalysis.bean.shared.relation

Base class that specifies a relation between two doubles.

RelationBean() - Constructor for class RelationBean

RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold

Defines a constant threshold, and a relation to it.

RelationToConstant() - Constructor for class RelationToConstant

RelationToConstant(RelationBean, double) - Constructor for class RelationToConstant

RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold

A base class specifying threshold and a relation to it, allowing for tests of a value in relation to a threshold.

RelationToThreshold() - Constructor for class RelationToThreshold

RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective

Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)

RelationWithMatches() - Constructor for class RelationWithMatches

relativeMaskTo(BoundingBox) - Method in class ObjectMask

Creates a new object-mask with coordinates changed to be relative to another box.

relativePath() - Method in class MutableDirectory

relativePath() - Method in class RootDirectory

relativePath() - Method in class SubdirectoryBase

relativePositionTo(BoundingBox) - Method in class BoundingBox

The relative position of the corner to another bounding box.

relativePositionToBox(BoundingBox) - Method in class BoundingBox

A new bounding-box using relative position coordinates to another box.

relativeScale(Extent, Extent, boolean) - Static method in class RelativeScaleCalculator

Multiplexes between RelativeScaleCalculator.relativeScalePreserveAspectRatio(Extent, Extent) and RelativeScaleCalculator.relativeScale(Extent, Extent).

relativeScale(Extent, Extent) - Static method in class RelativeScaleCalculator

Calculates a scaling factor so as to scale source to target.

RelativeScaleCalculator - Class in org.anchoranalysis.spatial.scale

Determine the scaling-factor needed to scale an Extent to become equal in size to another Extent.

relativeScalePreserveAspectRatio(Extent, Extent) - Static method in class RelativeScaleCalculator

Calculates a scaling factor so as to maximally scale source to target - while preserving the aspect ratio.

RelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer

Constructs a name by finding the relative-path between the file and the input-directory.

RelativeToDirectory() - Constructor for class RelativeToDirectory

releaseKeepBest() - Method in class DualState

releaseKeepBest() - Method in class OptimizationStep

rememberConverted(NamedChannelsInput, U, StringBuilder) - Method in class SharedStateRememberConverted

Remembers a converted input.

remove(int) - Method in class ColorList

Remove an element at a particular index.

remove(T) - Method in class IntersectingObjects

Removes an object-mask, so that it is no longer considered in queries.

remove(int) - Method in class ObjectCollection

Removes the object at the specified position in the collection.

remove(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria

remove(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown

remove(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown

remove(int) - Method in class MarksWithEnergyBreakdown

remove(int) - Method in class MarksWithTotalEnergy

remove(int, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy

remove(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy

remove(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs

remove(EnergySavedInd, int) - Method in class EnergyMemoList

remove(int) - Method in class MemoList

remove(VoxelizedMarkMemo) - Method in class MemoList

remove(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList

remove(Object) - Method in class UpdatableMarksList

remove(int) - Method in class UpdatableMarksList

remove(int) - Method in class ColoredMarks

remove(int) - Method in class MarkCollection

remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks

remove(int) - Method in class ColoredOverlayCollection

remove(int) - Method in class OverlayCollection

remove(BoundingBox, T) - Method in class BoundingBoxRTree

Removes a particular item from the r-tree, identified by its bounding-box and payload.

remove(double, double, T) - Method in class IntervalRTree

Removes a particular item from the r-tree, identified by its interval and payload.

remove(Rectangle, T) - Method in class RTree

Removes a particular item from the r-tree, identified by its Rectangle and payload.

removeAll(Collection<?>) - Method in class UpdatableMarksList

removeAndUpdateEnergy(MarksFromPartition, ProposerContext) - Method in class KernelDeathPartition

removeAndUpdateEnergy(T, ProposerContext) - Method in class KernelDeath

removeAndUpdateEnergy(VoxelizedMarksWithEnergy, ProposerContext) - Method in class KernelDeathVoxelized

removeBelowThreshold(int) - Method in class Histogram

All values less than threshold are removed.

removeClosestToUnitZ() - Method in class ImageMoments

Removes the entry that is closest to having an eigenVector in direction (0,0,1).

removeEdge(V, V) - Method in class GraphWithoutPayload

Remove an edge between two vertices.

removeEdge(V, V) - Method in class GraphWithPayload

Remove an edge between two vertices.

removeExtension(String) - Static method in class ExtensionUtilities

Removes an extension from a filename or path.

removeExtension(Path) - Static method in class ExtensionUtilities

Like ExtensionUtilities.removeExtension(String) but accepts and returns a Path.

RemoveExtension - Class in org.anchoranalysis.plugin.io.bean.file.namer

Removes extensions from the identifier (but not from the file) and only if the extension hasn't already been removed upstream.

RemoveExtension(FileNamer) - Constructor for class RemoveExtension

RemoveExtension() - Constructor for class RemoveExtension

removeIfExists(T) - Method in class NameValueMap

Removes an element from the set, if it exists.

removeIfExists(FeatureList<FeatureInput>) - Method in class SharedFeatures

Remove all features, if they currently exist, from features.

RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split

Considers all possible pairs of objects in a provider, and removes any intersecting pixels

RemoveIntersectingVoxels() - Constructor for class RemoveIntersectingVoxels

removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class ObjectIntersectionRemover

removeLeadingPeriod(String[]) - Static method in class FormatExtensions

Creates a set of extensions with the leading period.

removeLeft(int) - Method in class ContiguousVoxelPath

Removes the first numToRemove pixels from the left

RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.file.provider

RemoveMatching() - Constructor for class RemoveMatching

removeNonMatching(List<T>) - Method in class FilterDescriptiveNameEqualsContains

removeOrReplace(boolean, boolean, boolean) - Method in class MergeCandidate

Chops of one-side of keep, and one-side of merge

RemovePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition

RemovePartition() - Constructor for class RemovePartition

RemovePartitionAndThen<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition

RemovePartitionAndThen() - Constructor for class RemovePartitionAndThen

removeRight(int) - Method in class ContiguousVoxelPath

Removes the last numToRemove pixels from the right

RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter

Considers all possible pairs of objects in a provider, and removes those that touch the border.

RemoveTouchingBorder() - Constructor for class RemoveTouchingBorder

removeTouchingBorderXY(Extent) - Method in class OverlappingObjects

Removes any objects from the assignment if they touch the X or Y scene border.

RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive

RemoveTrailingDirectory() - Constructor for class RemoveTrailingDirectory

removeTwo(EnergyMemoList, int, int, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown

removeTwo(int, int, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy

removeTwo(EnergySavedInd, int, int) - Method in class EnergyMemoList

removeTwo(int, int) - Method in class MarkCollection

removeVertex(V) - Method in class GraphWithoutPayload

Removes a vertex and any edges connected to it.

removeVertex(V) - Method in class GraphWithPayload

Removes a vertex and any edges connected to it.

RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming

Removes any whitespace characters from the path

RemoveWhitespace() - Constructor for class RemoveWhitespace

Repeat - Class in org.anchoranalysis.bean.shared.color.scheme

Duplicates a ColorList produced by another ColorScheme a certain number of times.

Repeat() - Constructor for class Repeat

repeat(int, CheckedRunnable<E>) - Static method in class FunctionalIterate

Repeats an operation a number of times.

repeat(int, Supplier<T>) - Static method in class FunctionalList

Creates a list of elements, by repeatedly calling the same operation.

Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary

Repeat() - Constructor for class Repeat

Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection

Repeat() - Constructor for class Repeat

Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single

Repeat() - Constructor for class Repeat

Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position

Repeat() - Constructor for class Repeat

repeatCountSuccessful(int, CheckedBooleanSupplier<E>) - Static method in class FunctionalIterate

Repeats an operation a number of times, counting the number of times the operation returns true.

RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice

Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel

RepeatSlice() - Constructor for class RepeatSlice

RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice

Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask

RepeatSlice() - Constructor for class RepeatSlice

repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class FunctionalIterate

Repeats an operation until a true value is returned.

repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class FunctionalIterate

Repeats an operation a number of times, passing an increment index to operation each time.

Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive

Generates a file-path by replacing all occurrences of a string-pattern with another

Replace() - Constructor for class Replace

replaceBackslashes(String) - Static method in class SingleFile

replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class Mask

Replaces the underlying voxels in the mask with new voxels.

replaceError(ErrorNode) - Method in class ProposerContext

replaceError(ErrorNode) - Method in class KernelCalculationContext

replaceError(ErrorNode) - Method in class TransformationContext

ReplaceInfinity<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace

ReplaceInfinity() - Constructor for class ReplaceInfinity

replaceInput(T) - Method in class SessionInputSequential

Replaces existing input with new input

replaceInputManager(InputManager<?>) - Method in class InputOutputExperiment

ReplaceInputManager - Interface in org.anchoranalysis.experiment.io

Indicates and provides a mechanism that the InputManager can be replaced.

replaceInputManager(InputManager<?>) - Method in interface ReplaceInputManager

replaceInputManager(InputManager<?>) - Method in class QuickMultiDatasetExperiment

replaceInputManager(InputManager<?>) - Method in class QuickMultiDatasetStructuredExperiment

replaceMaxDirDepth(int) - Method in class PathMatchConstraints

ReplaceNaN<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace

ReplaceNaN() - Constructor for class ReplaceNaN

replaceOutputManager(OutputManager) - Method in class InputOutputExperiment

ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io

Indicates and provides a mechanism that the OutputManager can be replaced.

replaceOutputManager(OutputManager) - Method in interface ReplaceOutputManager

replaceOutputManager(OutputManager) - Method in class QuickMultiDatasetExperiment

replaceOutputManager(OutputManager) - Method in class QuickMultiDatasetStructuredExperiment

ReplacePropertyBeanFactory<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.xml.factory

Replaces a property (an XML element of attribute) on a bean before loading it.

ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class ReplacePropertyBeanFactory

replaceSlice(int, VoxelBuffer<T>) - Method in class BoundedVoxels

Assigns a new buffer for a slice.

replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class FromByte

replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class FromFloat

replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class FromInt

replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class FromShort

replaceSlice(int, VoxelBuffer<T>) - Method in interface SliceBufferIndex

Replaces the voxels for a particular z-slice.

replaceSlice(int, VoxelBuffer<T>) - Method in class Voxels

Assigns a new buffer for a particular slice.

replaceSlice(int, VoxelsUntyped, int, boolean) - Method in class VoxelsUntyped

Copies one particular z-slice of voxels from a source into the current voxels.

ReplaceStrategy<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.replace

replaceTask(Task<T, S>) - Method in class InputOutputExperiment

replaceTask(Task<T, S>) - Method in class JobProcessor

ReplaceTask<T extends InputFromManager,S> - Interface in org.anchoranalysis.experiment.io

Indicates and provides a mechanism that the Task can be replaced.

replaceTask(Task<T, S>) - Method in interface ReplaceTask

replaceTask(Task<U, S>) - Method in class ConvertNamedChannels

ReplaceUnusualValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace

Calculates the underlying feature, but replaces the result with a constant if it happens to be an "unusual" value

ReplaceUnusualValue() - Constructor for class ReplaceUnusualValue

replaceVoxels(Voxels<?>) - Method in class Channel

Assigns new voxels to replace the existing voxels.

replaceVoxels(Voxels<T>) - Method in class BoundedVoxels

Replaces the voxels in the box.

replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class ObjectMask

Replaces the voxels in the object-mask.

reportBegin(FeedbackBeginParameters<T>) - Method in class FeedbackReceiverList

reportBegin(FeedbackBeginParameters<T>) - Method in class FeedbackReceiverRequireArguments

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter

reportBegin(FeedbackBeginParameters<T>) - Method in class ReporterAggregate

reportBegin(FeedbackBeginParameters<T>) - Method in interface FeedbackReceiver

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter

reportBegin(FeedbackBeginParameters<T>) - Method in class NullReporter

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TextFile

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries

reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter

reportEnd(FeedbackEndParameters<T>) - Method in class FeedbackReceiverList

reportEnd(FeedbackEndParameters<T>) - Method in class FeedbackReceiverRequireArguments

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter

reportEnd(FeedbackEndParameters<T>) - Method in class ReporterAggregate

reportEnd(FeedbackEndParameters<T>) - Method in interface FeedbackReceiver

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter

reportEnd(FeedbackEndParameters<T>) - Method in class NullReporter

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class TextFile

reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter

ReporterAggregate<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback

ReporterAggregate(double) - Constructor for class ReporterAggregate

ReporterAggregate() - Constructor for class ReporterAggregate

ReporterException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback

ReporterException(String) - Constructor for exception ReporterException

ReporterException(Throwable) - Constructor for exception ReporterException

ReporterInterval<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback

ReporterInterval() - Constructor for class ReporterInterval

ReporterInterval(double) - Constructor for class ReporterInterval

ReportFeature<T> - Class in org.anchoranalysis.io.output.bean

ReportFeature() - Constructor for class ReportFeature

ReportFeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureEvaluator() - Constructor for class ReportFeatureEvaluator

ReportFeatureForManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report

ReportFeatureForManifest() - Constructor for class ReportFeatureForManifest

ReportFeatureForManifestFileBase - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report

ReportFeatureForManifestFileBase() - Constructor for class ReportFeatureForManifestFileBase

ReportFeatureForMarks<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureForMarks() - Constructor for class ReportFeatureForMarks

ReportFeatureForSharedObjects - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureForSharedObjects() - Constructor for class ReportFeatureForSharedObjects

ReportFeatureOnMark - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureOnMark() - Constructor for class ReportFeatureOnMark

ReportFeatureOnMarks - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureOnMarks() - Constructor for class ReportFeatureOnMarks

ReportFeatureOnObject - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureOnObject() - Constructor for class ReportFeatureOnObject

ReportFeatureOnObjectCollection - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureOnObjectCollection() - Constructor for class ReportFeatureOnObjectCollection

ReportFeatureOnObjectsBase<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureOnObjectsBase() - Constructor for class ReportFeatureOnObjectsBase

ReportFeatureWrapError - Class in org.anchoranalysis.mpp.io.bean.report.feature

ReportFeatureWrapError() - Constructor for class ReportFeatureWrapError

reporting(int, StateReporter<T, U>, TransformationContext) - Method in class OptimizationStep

Reporting<S> - Class in org.anchoranalysis.mpp.segment.optimization.step

Exposes data which is only needed by reporting tools

reportItr(Reporting<T>) - Method in class FeedbackReceiverList

reportItr(Reporting<T>) - Method in class FeedbackReceiverRequireArguments

reportItr(Reporting<T>) - Method in class ReporterInterval

reportItr(Reporting<T>) - Method in interface FeedbackReceiver

reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted

reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest

reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter

reportItr(Reporting<T>) - Method in class NullReporter

reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter

reportNewBest(Reporting<T>) - Method in class FeedbackReceiverList

reportNewBest(Reporting<T>) - Method in class FeedbackReceiverRequireArguments

reportNewBest(Reporting<T>) - Method in interface FeedbackReceiver

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class Log4JReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class MemoryUsageReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter

reportNewBest(Reporting<T>) - Method in class NullReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFile

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter

reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter

requestOmitExperimentIdentifier() - Method in class OutputArguments

requestOmitExperimentIdentifier() - Method in class OutputPrefixerSettings

requestOutputIncrementingNumberSequence() - Method in class OutputArguments

requestOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings

requestOutputSuppressDirectories() - Method in class OutputArguments

requestOutputSuppressDirectories() - Method in class OutputPrefixerSettings

RequireArguments - Class in org.anchoranalysis.experiment.bean.require

RequireArguments() - Constructor for class RequireArguments

RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require

RequireDebugMode() - Constructor for class RequireDebugMode

RequireFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.provider.single

RequireFeatureRelationThreshold() - Constructor for class RequireFeatureRelationThreshold

requiresImageMetadata() - Method in class SummarizerImageMetadata

requiresImageMetadata() - Method in class ExtractIdentifier

requiresImageMetadata() - Method in class ExtractIdentifierAndPath

requiresImageMetadata() - Method in class ExtractPath

requiresImageMetadata() - Method in class SummarizerPath

requiresImageMetadata() - Method in class Summarizer

Whether a ImageMetadataInput is required as an input.

requiresImageMetadata() - Method in class SummarizerAggregate

requiresImageMetadata() - Method in class SummarizerCount

requiresImageMetadata() - Method in class SummarizerListMultiline

requiresImageMetadata() - Method in class SummarizerSplitMoreThan

reset() - Method in class CachedSupplierBase

Ensures the object is unevaluated, deleting any cached result if it exists.

reset() - Method in class RunningSum

Reset the sum and count to zero.

reset() - Method in class RunningSumCollection

Resets all items to zero.

reset() - Method in class Histogram

Sets the count for all values to 0.

reset() - Method in class VoxelizedMarkMemo

reset() - Method in class AggIDCounter

reset() - Method in class Aggregator

reset() - Method in class PeriodTriggerBank

resetInd() - Method in class EnergySavedInd

ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache

A calculation that be invalidated (resetted), removing any existing cached value.

resizedXY(int, int, Interpolator) - Method in interface VoxelsExtracter

Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.

resizeXY(Extent) - Method in class Channel

Resizes the dimensions of the channel, interpolating the existing voxel values to match.

resizeXY(Extent, Interpolator) - Method in class Channel

Like Channel.resizeXY(Extent) but allows an explicit choice of Interpolator.

resizeXY(int, int) - Method in class Channel

Like Channel.resizeXY(Extent) but specifies the size via int parameters.

resizeXY(int, int, Interpolator) - Method in class Channel

Like Channel.resizeXY(Extent, Interpolator) but specifies the size via int parameters.

resizeXY(int, int) - Method in class Dimensions

Resizes the dimensions to have new sizes in the X and Y dimension.

resolution() - Method in class EnergyStack

The image-resolution associated with the energy-stack.

resolution() - Method in class Channel

The resolution of the voxel that describes a physical size for each voxel.

resolution() - Method in class Dimensions

Resolution of voxels to physical measurements.

resolution(Resolution) - Method in enum OrientationChange

A Resolution that describes resolution after the orientation change.

Resolution - Class in org.anchoranalysis.image.core.dimensions

The resolution of an image.

Resolution() - Constructor for class Resolution

Creates with a default resolution with value 1.0 in each dimension.

Resolution(double, double, double) - Constructor for class Resolution

Creates with a resolution from three double values for each dimension.

Resolution(Tuple3d) - Constructor for class Resolution

Constructs a resolution from a tuple.

resolution() - Method in class Mask

Resolution of voxels to physical measurements.

resolution() - Method in class DisplayStack

Resolution of voxels to physical measurements.

resolution() - Method in class Stack

Resolution of voxels to physical measurements.

ResolutionAsXml - Class in org.anchoranalysis.plugin.io.xml

Reads and writes a metadata XML file specifying the image-resolution.

resolutionRequired() - Method in class MergeBase

resolve(Path, Path) - Static method in class ResolvePathAbsolute

Like Path.resolve(java.nio.file.Path) but with some additional quirks.

resolve(Optional<UnitConverter>, DirectionVector) - Method in class DistancePhysical

resolve(Optional<UnitConverter>, DirectionVector) - Method in class DistanceVoxels

resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class UnitValueDistance

resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class UnitValueDistance

resolve(Optional<UnitConverter>, DirectionVector) - Method in class UnitValueDistance

resolve(Optional<Resolution>, boolean) - Method in class Bound

resolveArea(double, Optional<Resolution>) - Method in class FeatureSingleMemoRegion

resolveArea(double, Optional<Resolution>) - Method in class UnitConverter

Convert area into another unit representation

ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound

A bound resolved into pixel units

ResolvedBound(ResolvedBound) - Constructor for class ResolvedBound

ResolvedBound() - Constructor for class ResolvedBound

ResolvedBound(double, double) - Constructor for class ResolvedBound

resolveDistance(double, Optional<Resolution>, DirectionVector) - Method in class UnitConverter

Convert distance into another unit representation

ResolvedPart<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.cache.part

Like a CalculationPart but has been resolved against a cache to reuse any existing identical instance.

ResolvedPart(CalculationPart<S, T>) - Constructor for class ResolvedPart

ResolvedPartMap<S,T extends FeatureInput,U> - Class in org.anchoranalysis.feature.calculate.cache.part

A CalculationPartMap that has been resolved against a cache.

ResolvedPartMap(CalculationPartMap<S, T, U, FeatureCalculationException>) - Constructor for class ResolvedPartMap

Creates with a map.

resolveFeatureIdentifier(String) - Method in interface FeatureSymbolCalculator

Resolves an identifier to a unique-string, suitable for FeatureSymbolCalculator.calculateFeatureByIdentifier(String, FeatureCalculationInput).

resolveForAxis(Optional<UnitConverter>, Axis) - Method in class UnitValueDistance

Resolves the distance in a direction aligned to a particular axis

resolveName(String) - Method in class DefineAdderWithPrefixBean

Prepends a prefix before the name.

resolvePath(Path) - Method in class PathPrefixer

Converts a relative-path to an absolute-path (relative to the file-path associated with this current bean)

resolvePath(String) - Method in class PathPrefixer

An absolute path to the prefix

ResolvePathAbsolute - Class in org.anchoranalysis.core.system.path

More advanced implementation of Path.resolve(java.nio.file.Path).

resolver() - Method in interface FeatureCalculationInput

A resolver for calculations.

resolver() - Method in class SessionInputSequential

resolveTestPath(String) - Method in class TestLoader

Resolves a path to test-data (relative path to the test-data root) to an absolute path on the file system.

resolveToVoxels(Optional<UnitConverter>) - Method in class AreaPhysical

resolveToVoxels(Optional<UnitConverter>) - Method in class AreaPixels

resolveToVoxels(Optional<UnitConverter>) - Method in class UnitValueAreaOrVolume

Resolves a measurement of area/volume (in whatever units) to units corresponding to the image pixels/voxels.

resolveToVoxels(Optional<UnitConverter>) - Method in class VolumePhysical

resolveToVoxels(Optional<UnitConverter>) - Method in class VolumeVoxels

resolveVolume(double, Optional<Resolution>) - Method in class FeatureSingleMemoRegion

resolveVolume(double, Optional<Resolution>) - Method in class UnitConverter

Convert volume into another unit representation

resources() - Method in class LauncherConfig

Config for resources sued by the launcher

Resources - Class in org.anchoranalysis.launcher.resources

Accesses resource-files associated with this application.

Resources(ClassLoader, String, String, String, String, Optional<String>) - Constructor for class Resources

ResultsVector - Class in org.anchoranalysis.feature.results

A vector of results of applying a feature-calculations to many entities.

ResultsVector(int) - Constructor for class ResultsVector

Creates with a particular size.

ResultsVectorList - Class in org.anchoranalysis.feature.results

A list of elements of type ResultsVector.

ResultsVectorList(ResultsVector) - Constructor for class ResultsVectorList

Creates with the list containing a single item.

ResultsVectorList() - Constructor for class ResultsVectorList

ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins

ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature

A results-vector with an optional thumbnails associated with it.

ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>) - Constructor for class ResultsVectorWithThumbnail

ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Constructor for class ResultsVectorWithThumbnail

retainAll(Collection<?>) - Method in class UpdatableMarksList

RetrieveDestinationFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual

RetrieveDestinationFromDual() - Constructor for class RetrieveDestinationFromDual

RetrieveDestinationFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized

RetrieveDestinationFromVoxelized() - Constructor for class RetrieveDestinationFromVoxelized

RetrieveSingleMarkOnly - Class in org.anchoranalysis.plugin.mpp.bean.provider.single

Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an exception

RetrieveSingleMarkOnly() - Constructor for class RetrieveSingleMarkOnly

RetrieveSourceFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual

RetrieveSourceFromDual() - Constructor for class RetrieveSourceFromDual

RetrieveSourceFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized

RetrieveSourceFromVoxelized() - Constructor for class RetrieveSourceFromVoxelized

reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class BinaryVoxelsFactory

Like BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on (255).

reuseByte(Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Static method in class BinaryVoxelsFactory

Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing off and on.

reuseInt(Voxels<UnsignedIntBuffer>, BinaryValuesInt) - Static method in class BinaryVoxelsFactory

Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing off and on.

ReuseSingletonStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace

Always re-use a singleton SessionInput, invalidating it each time a new call occurs

ReuseSingletonStrategy(CacheCreator) - Constructor for class ReuseSingletonStrategy

Constructor with default means of creating a session-input

ReuseSingletonStrategy(CacheCreator, ChildCacheFinder) - Constructor for class ReuseSingletonStrategy

Constructor with custom means of creating a session-input

reverse() - Method in class MergeCandidate

reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class FunctionalIterate

Iterates through every element in an array in reverse order

rewind() - Method in class UnsignedByteBuffer

Rewinds the buffer ala Buffer.rewind().

rgb(boolean) - Method in class StackWriteAttributes

Derives a StackWriteAttributes that will be RGB, but is otherwise unchanged.

rgb(boolean, boolean) - Static method in class StackWriteAttributesFactory

RGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle

Converts a set of channels to a single RGB-stack.

RGB() - Constructor for class RGB

RGBChannelNames - Class in org.anchoranalysis.image.core.stack

Constants for referring to the channels in a RGB-stack or RGBA-stack.

RGBColor - Class in org.anchoranalysis.core.color

A color encoded in RGB color space.

RGBColor() - Constructor for class RGBColor

Create with black color.

RGBColor(Color) - Constructor for class RGBColor

Create from a Color.

RGBColor(int) - Constructor for class RGBColor

Creates with an RGB value encoded as an int, as in the constructor for Color.

RGBColor(int, int, int) - Constructor for class RGBColor

Creates with specific values for the red, green and blue components.

RGBColorBean - Class in org.anchoranalysis.bean.shared.color

A bean describing a color in the RGB color space.

RGBColorBean() - Constructor for class RGBColorBean

Creates with a completely black color.

RGBColorBean(RGBColor) - Constructor for class RGBColorBean

Create from a RGBColor.

RGBColorBean(Color) - Constructor for class RGBColorBean

Create from a Color.

RGBColorBean(int, int, int) - Constructor for class RGBColorBean

Create from values for red, green and blue.

rgbMaybe3D(boolean) - Static method in class StackWriteAttributesFactory

RGBStack - Class in org.anchoranalysis.image.core.stack

A stack with exactly three channels, respectively for red, green and blue colors.

RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class RGBStack

Creates a particularly-sized stack with all channels initialized to 0.

RGBStack(Stack) - Constructor for class RGBStack

Creates from an existing stack (which must have 1 or 3 channels).

RGBStack(Channel, Channel, Channel) - Constructor for class RGBStack

Create with Channels for each color.

RGBTimeSeriesGenerator - Class in org.anchoranalysis.image.io.stack.output.generator

RGBTimeSeriesGenerator(StackWriteOptions) - Constructor for class RGBTimeSeriesGenerator

rightSize() - Method in class OverlappingObjects

The total number of objects in the right set.

rmv(int) - Method in class EnergySavedInd

rmvFromUpdatablePairList(UpdatableMarksList, Mark) - Method in class VoxelizedMarksWithEnergy

rootDirectory(InputContextParameters) - Method in class FilesProvider

A root directory for these files, if it exists.

rootDirectory(InputContextParameters) - Method in class FilesProviderUnary

rootDirectory(InputContextParameters) - Method in class FilesProviderWithDirectory

rootDirectory(InputContextParameters) - Method in class FilesProviderWithoutDirectory

rootDirectory(InputContextParameters) - Method in class SpecificPathList

RootDirectory - Class in org.anchoranalysis.io.manifest.directory

RootDirectory() - Constructor for class RootDirectory

RootDirectory(Path) - Constructor for class RootDirectory

rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class PathPrefixer

Provides a prefix that becomes the root-folder.

rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve

rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory

rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class Rooted

rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure

rootDirectoryPrefixAvoidResolve(Optional<String>) - Method in class PathPrefixerAvoidResolve

Provides a prefix that becomes the root-folder.

Rooted - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer

Prepend a 'root' before the file-path-prefix obtained from a delegate

Rooted() - Constructor for class Rooted

Rooted(PathPrefixerAvoidResolve, String) - Constructor for class Rooted

Rooted - Class in org.anchoranalysis.plugin.io.bean.file.provider

Represents a set of files, with a different path-root depending on context.

Rooted() - Constructor for class Rooted

Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive

Rooted() - Constructor for class Rooted

RootedExperiment - Class in org.anchoranalysis.plugin.quick.bean.structure

RootedExperiment() - Constructor for class RootedExperiment

RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path

RootedFilePath() - Constructor for class RootedFilePath

RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path

RootFilePathRegEx - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report

RootFilePathRegEx() - Constructor for class RootFilePathRegEx

RootPath - Class in org.anchoranalysis.bean.shared.path

Defines a root path.

RootPath() - Constructor for class RootPath

RootPathMap - Class in org.anchoranalysis.plugin.io.input.path

A collection of root-paths indexed by their name.

RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points

A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.

RotatableBoundingBox() - Constructor for class RotatableBoundingBox

RotatableBoundingBoxFactory - Class in org.anchoranalysis.mpp.mark.points

Creates instances of RotatableBoundingBox.

RotateImageToMatchEXIFOrientation - Class in org.anchoranalysis.plugin.io.bean.stack.reader

Rotates an image to match any EXIF orientation information, if it exists.

RotateImageToMatchEXIFOrientation() - Constructor for class RotateImageToMatchEXIFOrientation

RotateImageToMatchEXIFOrientation(StackReaderOrientationCorrection) - Constructor for class RotateImageToMatchEXIFOrientation

rotatePoint(Tuple3d) - Method in class RotationMatrix

Performs a rotation on a single point, encoded as a Point3d.

rotatePointInplace(Point3d) - Method in class RotationMatrix

Performs a rotation on a single point, replacing the existing value of the point.

RotationMatrix - Class in org.anchoranalysis.spatial.orientation

A matrix that performs a rotation in Euclidean space.

RotationMatrix(int) - Constructor for class RotationMatrix

Creates a rotation-matrix populated only with zeros.

RotationMatrix(DoubleMatrix2D) - Constructor for class RotationMatrix

Creates a rotation-matrix from an existing DoubleMatrix2D.

RowLabels - Class in org.anchoranalysis.feature.io.csv

Labels for each row of feature-results in the outputted CSV row.

RowLabels(String) - Constructor for class RowLabels

Creates with a single string as an identifier.

RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class RowLabels

RTree<T> - Class in org.anchoranalysis.spatial.rtree

Bases class for implementations of R-Trees that store objects with associated geometry.

RTree(int) - Constructor for class RTree

Creates an empty R-Tree.

RTree(int, int) - Constructor for class RTree

Creates an empty R-Tree with a specified number of children.

run() - Method in interface CheckedRunnable

Runs an operation like with Runnable.run().

runCommandLineApplication(String[], LauncherConfig, Logger) - Static method in class Launch

Runs a command-line application, by parsing arguments, and then executing an experiment.

runExperiment(String) - Method in class ExperimentLauncherFromShell

Runs an experiment identified by an XML found in the resources

runExperiment(String, Optional<String>, Optional<String>) - Method in class ExperimentLauncherFromShell

Runs an experiment identified by an XML found in the resources

runExperimentInTemporaryDirectory(String, Path) - Method in class ExperimentLauncherFromShell

Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment

runExperimentInTemporaryDirectory(String, Optional<String>, Optional<String>, Path, String[]) - Method in class ExperimentLauncherFromShell

Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment

RunningSum - Class in org.anchoranalysis.math.arithmetic

Mutable class that allows for incrementing jointly sum and count variables, so as to eventually calculate the mean.

RunningSum() - Constructor for class RunningSum

RunningSum(double, long) - Constructor for class RunningSum

RunningSumCollection - Class in org.anchoranalysis.math.arithmetic

A collection of RunningSum where an operation is executed on all objects in the collection.

RunningSumCollection(int) - Constructor for class RunningSumCollection

Constructor.

RunningSumExtrema - Class in org.anchoranalysis.math.arithmetic

Like a RunningSum but also remembers the mean and max across all the added values.

RunningSumExtrema() - Constructor for class RunningSumExtrema

RunningSumParented - Class in org.anchoranalysis.experiment.time

Wraps a RunningSum with an additional variable, indicating the total number of parent operations.

RunningSumParented(int) - Constructor for class RunningSumParented

RunningSumPoint - Class in org.anchoranalysis.spatial.point

A running sum for tracking points separately in each dimension.

RunningSumPoint() - Constructor for class RunningSumPoint

runTaskAndCompareOutputs(T, V, Path, String, Iterable<String>) - Static method in class TaskSingleInputHelper

Executes a task on a single-input.

S

sampleDoubleFromRange(double) - Method in interface RandomNumberGenerator

Generates a uniformly random floating-point number within a range from 0 (exclusive) to endExclusive.

sampleDoubleFromRange(double, double) - Method in interface RandomNumberGenerator

Generates a uniformly random floating-point number within a range.

sampleDoubleFromZeroCenteredRange(double) - Method in interface RandomNumberGenerator

Generates a uniformly random floating-point number centered around 0 ranging from [-halfWidth,+halfWidth] (both exclusive).

sampleDoubleZeroAndOne() - Method in interface RandomNumberGenerator

Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0 (exclusive).

sampleDoubleZeroAndOne() - Method in class RandomNumberGeneratorMersenne

sampleFromAvailable(int) - Method in class PartitionedMarks

Samples from the available marks

sampleFromList(List<T>) - Method in interface RandomNumberGenerator

Samples uniformly an element from a list.

sampleInteger(int) - Method in class ProposerContext

Samples an integer uniformally between [0..maxVal)

sampleIntFromRange(int) - Method in interface RandomNumberGenerator

Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.

sampleIntFromRange(int, int) - Method in interface RandomNumberGenerator

Samples from a uniformly random discrete number within a range.

sampleLongFromRange(long) - Method in interface RandomNumberGenerator

Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.

sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollectionWithAddCriteria

sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollection

SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider

SampleWithDirectory() - Constructor for class SampleWithDirectory

ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer

ScalarProposer() - Constructor for class ScalarProposer

ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer

Like a IntConsumer but accepts three coordinates of a point as scalar arguments.

ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer

Like a IntConsumer but accepts two coordinates of a point as scalar arguments.

scale(ScaleFactor, Interpolator, Optional<Extent>) - Method in class BoundedVoxels

Creates a scaled-version (in XY dimensions only) of the current bounding-box.

scale(ScaleFactor) - Method in class ObjectMask

Produces a scaled-version of an object-mask.

scale(ScaleFactor, Optional<Extent>) - Method in class ObjectMask

Produces a scaled-version of an object-mask.

scale(double) - Method in class Bound

scale(double) - Method in class BoundMinMax

scale(double) - Method in class ResolvedBound

scale(ScaleFactor) - Method in class Ellipse

scale(ScaleFactor) - Method in class Ellipsoid

scale(ScaleFactor) - Method in class MarkWithPositionAndSingleRadius

Objects are scaled in pre-rotated position.

scale(ScaleFactor) - Method in class Mark

Scales the mark in X and Y dimensions.

scale(ScaleFactor) - Method in class MarkWithPosition

scale(ScaleFactor) - Method in class LineSegment

scale(ScaleFactor) - Method in class PointList

scale(ScaleFactor) - Method in class Polygon

scale(ScaleFactor) - Method in class PolygonCurve

scale(ScaleFactor) - Method in class RotatableBoundingBox

scale(Channel, ScaleCalculator, Interpolator, Optional<ImageSizeSuggestion>, MessageLogger) - Static method in class ScaleXY

scale(Mask, ScaleCalculator, Optional<ImageSizeSuggestion>) - Static method in class ScaleXY

Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider

Scales all the objects in the collection by a particular scale-factor.

Scale() - Constructor for class Scale

Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar

Scale() - Constructor for class Scale

scale(ScaleFactor) - Method in class BoundingBox

Scales the bounding-box, both the corner-point and the extent.

scale(ScaleFactor, Extent) - Method in class BoundingBox

Scales the bounding-box corner-point, and assigns a new extent.

scale(double) - Method in class Point2d

Arithmetically multiplies each dimension's value by a factor.

scale(double) - Method in class Point2f

Multiplies each dimension's component by a factor.

scale(double) - Method in class Tuple3d

Arithmetically multiply values across each dimension.

scale(int) - Method in class Tuple3i

Arithmetically multiplies by a value across each dimension.

scale(double) - Method in class Tuple3i

Arithmetically multiplies by a value across each dimension.

scale(Point3d) - Method in class ScaleFactor

Multiplies a Point3d by the respective scaling-factor in each X and Y dimensions.

scale(int, int) - Method in class ScaleFactorInt

Multiplies a point by the respective scaling-factor in each dimension.

scale(Point2i) - Method in class ScaleFactorInt

Multiplies a Point2i by the respective scaling-factor in each dimension.

scale(Extent) - Method in class ScaleFactorInt

Multiplies an Extent by the respective scaling-factor in each dimension.

scale(ScaleFactor, Point3i) - Static method in class Scaler

Scales a point in XY by multiplying each dimension by its corresponding scaling-factor.

ScaleableBackground - Class in org.anchoranalysis.image.io.stack.output.box

A stack that can be used as a background (and maybe scaled).

scaleBy(DisplayStack, ScaleFactor, Interpolator) - Static method in class ScaleableBackground

Creates a background from a stack with scaling

ScaleByDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.convert

Scales by compressing a certain range of values into the 8-bit signal.

ScaleByDictionary() - Constructor for class ScaleByDictionary

ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert

Scales by compressing a certain range of values into the 8-bit signal

ScaleByMinMaxValue() - Constructor for class ScaleByMinMaxValue

ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert

ScaleByTypeToByte() - Constructor for class ScaleByTypeToByte

ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial

Calculating a scaling-factor from dimensions.

ScaleCalculator() - Constructor for class ScaleCalculator

scaleClampTo(ScaleFactor, Extent) - Method in class BoundingBox

Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a containing-extent.

ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale

A list of elements, with an ObjectMask representation, that have been scaled.

ScaledElements(List<T>, ScaleFactor, ObjectScalingMethod, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Constructor for class ScaledElements

Creates elements to be scaled.

scaledObjectFor(T) - Method in class ScaledElements

Gets the scaled version of an element given the unscaled element.

ScaledOverlayCreator - Interface in org.anchoranalysis.overlay.object.scaled

Creates a scaled version of ObjectMask to use as an overlay.

scaleElements(List<T>, ScaleFactor, AccessObjectMask<T>) - Method in interface ObjectScalingMethod

Applies a scaling factor to elements, where each element is associate with a unique ObjectMask.

scaleElements(List<T>, ScaleFactor, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Method in interface ObjectScalingMethod

Applies a scaling factor to elements, where each element is associate with a unique ObjectMask.

scaleElements(List<T>, ScaleFactor, boolean, Extent, AccessObjectMask<T>) - Static method in class Scaler

Scales every element in a list collectively, ensuring the results remain inside a particular region.

ScaleFactor - Class in org.anchoranalysis.spatial.scale

What to scale X and Y dimensions by.

ScaleFactor(double) - Constructor for class ScaleFactor

Create with an identical scaling-factor for all dimensions.

ScaleFactor(double, double) - Constructor for class ScaleFactor

Create with specific scaling-factors for each dimension.

ScaleFactorInt - Class in org.anchoranalysis.spatial.scale

Like ScaleFactor but only allows integer scaling-factors in each dimension.

ScaleFactorInt(int, int) - Constructor for class ScaleFactorInt

ScaleImage - Class in org.anchoranalysis.plugin.image.task.bean.scale

Creates a scaled copy of images.

ScaleImage() - Constructor for class ScaleImage

scaleObjects(ObjectCollection, ScaleFactor) - Static method in class Scaler

Scales every object-mask in a collection collectively.

scaleObjects(ObjectCollection, ScaleFactor, boolean, Extent) - Static method in class Scaler

Scales every object-mask in a collection collectively, ensuring the results remain inside a particular region.

scaleObjects(ObjectCollection, ScaleFactor, boolean, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class Scaler

Scales every object-mask in a collection collectively (if not overlappjng), allowing for additional manipulation before and after scaling.

scaleQuantity(double, int) - Static method in class Scaler

Multiplies a quantity (integer) by a scaling-factor, returning it as an integer.

Scaler - Class in org.anchoranalysis.image.core.object.scale

Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.

Scaler - Class in org.anchoranalysis.spatial.scale

Scales different types of entities with a ScaleFactor.

scaleRadii(double) - Method in class Ellipse

ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack

Create a thumbnail by scales an image to a particular size.

ScaleToSize() - Constructor for class ScaleToSize

scaleX(double) - Method in class Tuple3i

Arithmetically multiplies the X-axis component by a value.

scaleXY(ScaleFactor) - Method in class DualMarksAnnotation

Scales the marks in the annotation in X and Y dimensions.

scaleXY(ScaleFactor) - Method in class Channel

Resizes the dimensions of the channel, by scaling the existing size by a factor.

scaleXY(ScaleFactor, Interpolator) - Method in class Channel

Like Channel.scaleXY(ScaleFactor) but allows an explicit choice of Interpolator.

scaleXY(ScaleFactor) - Method in class Resolution

Multiplies the X and Y components of the resolution by a factor.

scaleXY(ScaleFactor) - Method in class Mask

Creates a new Mask whose X- and Y- dimensions are scaled by scaleFactor.

scaleXY(ScaleFactor) - Method in class MarkCollection

Scales the mark in X and Y dimensions.

ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity

Scales the channel in the X and Y dimensions.

ScaleXY() - Constructor for class ScaleXY

ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider

Scales the mask in XY dimensions, but not in Z dimension.

ScaleXY() - Constructor for class ScaleXY

ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection

ScaleXY() - Constructor for class ScaleXY

scaleXY(double) - Method in class Tuple3d

Arithmetically multiply values by a factor only in X and Y dimensions.

scaleXY(double) - Method in class Tuple3i

Arithmetically multiplies the X- and Y-axis components by a value.

scaleXYBy(ScaleFactor) - Method in class Dimensions

Scales the X- and Y- dimensions by a scaling-factor.

scaleXYBy(ScaleFactor) - Method in class Extent

Scales the X- and Y- dimensions by a scaling-factor.

scaleY(double) - Method in class Tuple3i

Arithmetically multiplies the Y-axis component by a value.

scaling - Variable in class ToUnsignedByteWithScaling

sceneContains(Point2i) - Static method in class CircleObjectFixture

ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score

ScoreObjects() - Constructor for class ScoreObjects

ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score

Assigns a score (a value indicating how probable something is) to each voxel

ScoreVoxels() - Constructor for class ScoreVoxels

search(CalculationPart<S, T>) - Method in interface CalculationPartResolver

Searches for an equivalent calculation to calculation.

search(CalculationPartMap<S, T, U, FeatureCalculationException>) - Method in interface CalculationPartResolver

Searches for an equivalent calculation to calculation.

SearchDirectory - Class in org.anchoranalysis.io.input.bean.files

Searches a directory for files whose paths match a particular predicate.

SearchDirectory(String) - Constructor for class SearchDirectory

Create for a specific directory.

SearchDirectory() - Constructor for class SearchDirectory

Second - Class in org.anchoranalysis.image.feature.bean.object.pair

Evaluates the first-object in a pair only

Second(Feature<FeatureInputSingleObject>) - Constructor for class Second

Second() - Constructor for class Second

second(String) - Method in class MultiLevelBinary

second(String) - Method in class MultiLevelNot

second(String) - Method in interface MultiLevelOutputEnabled

A second-level of OutputEnabled for a particular outputName as used in first-level.

second(String) - Method in class OutputEnabledMutable

second(String) - Method in class MultiLevelRecordedOutputs

A RecordedOutputs for recording second-level outputs for a given outputName from the first-level.

secondaryReport() - Method in class StateReporter

secondaryReport() - Method in class StateReporterIdentity

secondaryReport() - Method in class StateReporterToPixelized

secondaryReport() - Method in class StateReporterTransformer

secondEntries() - Method in class MultiLevelRecordedOutputs

All second-level recorded output entries.

secondLevel(String) - Method in class RecordingWriters

A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.

secondLevelOutputs(String, OutputEnabled) - Method in class OutputEnableRulesSpecify

secondPart() - Method in class CombinedName

secondPart() - Method in interface MultiName

The second part of the name.

secondPart() - Method in class SimpleName

seek(int) - Method in class SlidingBuffer

Moves buffer to a particular z-slice.

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentation

Performs a segmentation on voxels so that each voxel has an on or off state after the operation.

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationOne

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationReference

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationThreshold

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class SegmentChannelIntoObjects

Segments a channel to produce an object-collection.

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class SegmentChannelIntoObjectsUnary

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary

segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentIntoMarks

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class AtScale

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class ConnectedComponentsFromBinarySegmentation

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class Filter

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class ImposeMinima

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class Mser

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class SegmentOnMaximumIntensityAndExpandInZ

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class WatershedYeong

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class Sequence

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class ThresholdAgainstChannel

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class FloodFillEachIntensityLevel

segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class SegmentThresholdAboveMinBound

segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentWithMarkedPointProcess

segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholder

segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderMask

segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderWithoutMask

SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment

Performs some kind of segmentation on an image.

SegmentationBean() - Constructor for class SegmentationBean

SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.error

SegmentationFailedException(String) - Constructor for exception SegmentationFailedException

SegmentationFailedException(String, Throwable) - Constructor for exception SegmentationFailedException

SegmentationFailedException(Throwable) - Constructor for exception SegmentationFailedException

SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Applies a BinarySegmentation algorithm to derive a mask from a channel

SegmentChannel() - Constructor for class SegmentChannel

SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment

SegmentChannel() - Constructor for class SegmentChannel

SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment

Performs segmentation of a channel using each object in the upstream collection as a mask.

SegmentChannelByObject() - Constructor for class SegmentChannelByObject

SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object

A base class for algorithms to segment a channel into one or more objects.

SegmentChannelIntoObjects() - Constructor for class SegmentChannelIntoObjects

SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object

A base-class for segmentations that takes another object-segmentation algorithm as a parameter.

SegmentChannelIntoObjectsUnary() - Constructor for class SegmentChannelIntoObjectsUnary

segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class BinarySegmentationOne

segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Invert

segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Repeat

SegmentInstanceWithModel<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.task.bean.segment

Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.

SegmentInstanceWithModel() - Constructor for class SegmentInstanceWithModel

SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean

SegmentIntoMarks() - Constructor for class SegmentIntoMarks

SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment

Segments an image into a collection of Marks.

SegmentMarksFromImage() - Constructor for class SegmentMarksFromImage

SegmentMarksState - Class in org.anchoranalysis.plugin.mpp.segment.shared

State that only needs to be initialized once can be shared across many calls to the algorithm.

SegmentMarksState(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>, Define) - Constructor for class SegmentMarksState

SegmentObjectsFromONNXModel - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.stack

Performs instance-segmentation using the ONNX Runtime and an .onnx model file.

SegmentObjectsFromONNXModel() - Constructor for class SegmentObjectsFromONNXModel

SegmentObjectsFromTensorFlowModel - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack

Performs instance-segmentation using OpenCV's DNN module and a TensorFlow .pb SavedModel file.

SegmentObjectsFromTensorFlowModel() - Constructor for class SegmentObjectsFromTensorFlowModel

SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel

Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.

SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class SegmentOnMaximumIntensityAndExpandInZ

SegmentStack<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment

Segments a stack into objects.

SegmentStack() - Constructor for class SegmentStack

SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary

SegmentThresholdAboveMinBound() - Constructor for class SegmentThresholdAboveMinBound

SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks

Segments a channel with a Marked Point Process.

SegmentWithMarkedPointProcess() - Constructor for class SegmentWithMarkedPointProcess

SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment

Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds

SegmentWithSeeds() - Constructor for class SegmentWithSeeds

select(ExecutionArguments) - Method in interface SelectParam

Retrieves the parameter.

select(ExecutionArguments) - Method in class UseDefaultManager

selectChannels(ChannelSource, boolean) - Method in class All

selectChannels(ChannelSource, boolean) - Method in class FromStacks

Takes a stack-collection and extracts a set of references to particular channels (each with a name)

selectChannels(ChannelSource, boolean) - Method in class One

selectChannels(ChannelSource, boolean) - Method in class SpecificAndRename

selectDelegate(StackWriteOptions) - Method in class BranchChannels

selectDelegate(StackWriteOptions) - Method in class BranchStack

selectDelegate(StackWriteOptions) - Method in class BranchSuggestedFormat

selectDelegate(StackWriteOptions) - Method in class StackWriterDelegateBase

Selects a StackWriter to use as a delegate.

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class HDF5ObjectsGenerator

selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGenerator

Selects the file-extension to use for a particular stack.

selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGeneratorSelectFormat

Combines stack-write-options derived for a particular stack with the general write-options associated with the RasterGenerator.

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class RGBTimeSeriesGenerator

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class DictionaryGenerator

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SerializedGenerator

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGenerator

Selects the file/extension to be used for outputting the file.

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGeneratorBridge

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class CSVGenerator

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class StringGenerator

selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class XMLGenerator

selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class KernelDeath

selective() - Method in class RecordingWriters

A writer that allows only certain selected output-names, and records the written output-names

selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposer

selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Check

selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposerUnary

selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class MarkFromCollectionProposerUnary

selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Repeat

selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class UniformRandom

selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class RecordedOutputsWithRules

Selects which OutputEnabledRules to employ.

SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam

Different methods of selecting a object T that is used as a parameter for an experiment.

SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam

Creates an appropriate SelectParam based upon the options passed to the command-line.

SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region

SelectSlicesBase() - Constructor for class SelectSlicesBase

SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region

SelectSlicesWithIndexBase() - Constructor for class SelectSlicesWithIndexBase

separate(Collection<T>) - Method in class SpatiallySeparate

Splits a collection of elements into spatially separate clusters, without consuming all elements in elements.

Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary

Performs a sequence of succesive segmentations

Sequence() - Constructor for class Sequence

SequencedDirectory - Interface in org.anchoranalysis.io.manifest.directory.sequenced

SequencedDirectoryDeserializer<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced

Applies a deserializer to each file in a directory with a sequence of files.

SequencedDirectoryDeserializer(SequencedDirectory, Deserializer<T>, Logger) - Constructor for class SequencedDirectoryDeserializer

Creates from a manifest-directory entry.

SequenceInteger - Class in org.anchoranalysis.bean.permute.property

A sequence of integers.

SequenceInteger() - Constructor for class SequenceInteger

sequenceIterator() - Method in class PermutePropertySequence

Iterates each element in sequence.

SequenceMemory - Class in org.anchoranalysis.io.generator.sequence

SequenceMemory() - Constructor for class SequenceMemory

SequenceType<T> - Class in org.anchoranalysis.io.manifest.sequencetype

A sequence of elements (of type T), which are mapped to a range of integer indices.

SequenceType() - Constructor for class SequenceType

SequenceTypeException - Exception in org.anchoranalysis.io.manifest.sequencetype

SequenceTypeException(String) - Constructor for exception SequenceTypeException

SequenceTypeException(Exception) - Constructor for exception SequenceTypeException

SequentialProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor

Executes jobs sequentially

SequentialProcessor() - Constructor for class SequentialProcessor

SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session

Calculates features with successively different parameters, taking care of caching etc.

SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized

SerializedGenerator(Optional<String>) - Constructor for class SerializedGenerator

SerializedObjectSupplier<T> - Interface in org.anchoranalysis.io.manifest.finder

Supplies a serialized-object (if it exists)

serializeObjectToFile(T, Path) - Static method in class XStreamSerializer

Writes a file with a serialized representation of an object.

SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session

A feature-input that will be used in a SequentialSession

SessionInputSequential(T, CacheCreator) - Constructor for class SessionInputSequential

Constructor

SessionInputSequential(T, CacheCreator, ChildCacheFinder) - Constructor for class SessionInputSequential

set() - Method in class DoubleSet

The underlying set of values.

set() - Method in class IntegerSet

The underlying set of values.

set() - Method in class StringSet

The underlying set of values.

set(int, double) - Method in class ResultsVector

Assigns a result at a particular position.

set(int, ResultsVector) - Method in class ResultsVector

Assigns many results, starting at a particular position, and incrementing thereafter.

set(int, VoxelizedMarkMemo) - Method in class MemoList

set(int, UpdatableMarks) - Method in class UpdatableMarksList

set(int, Mark) - Method in class MarkCollection

setAboveMaxValue(double) - Method in class RangeCompareBase

Constant to return if outside the range (above the maximum allowed)

setAcceptDirectoryErrors(boolean) - Method in class SearchDirectory

If true, continues when a directory-access-error occurs (logging it), otherwise throws an exception.

setAcceptMissingResolution(boolean) - Method in class WithResolutionBase

Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).

setAcceptMissingResolution(boolean) - Method in class VoxelPhysicalSize

Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).

setAcceptNoResolution(boolean) - Method in class ReadVoxelExtentXml

If false, an exception is thrown if the resolution file is missing for a particular image.

setAcceptOutsideScene(boolean) - Method in class CheckMarkWithMask

setAdd(DefineAdderBean) - Method in class VisualizeOnBackground

setAddCriteria(AddCriteria<T>) - Method in class RandomCollectionWithAddCriteria

setAdditionalBackgrounds(List<DerivePath>) - Method in class MarkProposerStrategy

Additional background-stacks that are possible to use while annotating.

setAdditionalChannels(List<ChannelEntry>) - Method in class MultiInputManagerQuick

Additional channels other than the main one, which are located in the main raster file

setAdditionalChannels(List<ChannelEntry>) - Method in class NamedChannelsQuick

Additional channels other than the main one, which are located in the main raster file

setAdditionalPropertyPaths(StringSet) - Method in class PermuteProperty

Additional property paths that are also changed, together with propertyPath.

setAddName(boolean) - Method in class CombineCSV

setAddOne(boolean) - Method in class Quantile

setAddSum(int) - Method in class GradientBaseAddSum

Added to all gradients (so we can store negative gradients)

setAdjacentChannels(List<AdjacentFile>) - Method in class NamedChannelsQuick

Channels that are located in a separate raster file adjacent to the main raster file

setAggIntervalLog10(double) - Method in class ReporterInterval

How many iterations before printing a new report? Encoded in log10.

setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class FeedbackBeginParameters

setAll(EnergySavedAll) - Method in class MarksWithEnergyBreakdown

Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component

setAnnealScheme(AnnealScheme) - Method in class SimulatedAnnealing

setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class FromAnnotations

setAnnotatorStrategy(S) - Method in class AnnotationInputManager

The strategy to be used for annotating.

setAppendChannels(List<AppendStack>) - Method in class NamedChannelsQuick

Channels that are located in a separate raster file somewhere else in the project's structure

setAppendCSV(DerivePath) - Method in class FromCSVInputManager

setAppendCsv(AppendCsv) - Method in class MatchedAppendCsv

setAppendDictionary(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendFilePath(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendMarks(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setAppendObjects(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

Appends object-collections to the MultiInput.

setAppendStack(List<NamedBean<DerivePath>>) - Method in class MultiInputManager

setApplyResolution(boolean) - Method in class DistanceTransform3D

Multiples the values by the x-resolution, if it exists.

setApplyToPath(boolean) - Method in class MatchRegularExpression

If true, the filter is applied to the path as a whole, not just the filename (using forward slashes as directory separators)

setArrange(ArrangeStackBean) - Method in class ArrangeRaster

setArrange(ArrangeStack) - Method in class Cell

setArrange(ArrangeStackBean) - Method in class CombineRasterGenerator

setAsMemberFlag(byte, byte) - Static method in class RegionMembershipUtilities

setAsPercentage(boolean) - Method in class Quantile

If true, the quantile is interpreted as a percentage rather than a decimal

setAssigner(AnnotationComparisonAssigner<T>) - Method in class CompareAnnotations

setAssignMode(AssignMode<S, T, U>) - Method in class SimulatedAnnealing

setAvoidBulletOnFirst(boolean) - Method in class SummarizerAggregate

Iff true no bullet is added for the very first-item in the list

setAvoidDivideByZero(boolean) - Method in class Divide

setAvoidOverlappingObjects(boolean) - Method in class PairNeighbors

If true, no overlapping objects are treated as pairs

setAxis(String) - Method in class AxisAlignedUnitVector

Which axis the unit-vector will align with.

setAxis(String) - Method in class CenterOfGravity

setAxis(String) - Method in class GradientForAxis

Which axis? X=0, Y=1, Z=2

setAxis(String) - Method in class ForSpecificAxis

setAxis(String) - Method in class ArbitraryInsidePoint

setAxis(String) - Method in class BoundingBoxAlongAxisBase

setAxis(String) - Method in class GradientMeanForAxis

setAxis(String) - Method in class PrincipalAxisOrientation

Which axis to read from (x,y,z)

setAxis(String) - Method in class BoundingBoxExtent

setAxisColor(RGBColorBean) - Method in class PlotColorScheme

setAxisMax(double) - Method in class AxisLimits

setAxisMin(double) - Method in class AxisLimits

setBackground(AnnotationBackground) - Method in class AnnotatorStrategy

The visual background to use while annotating.

setBackground(Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator

A background image or dimensions to define an empty background.

setBackground(String) - Method in class CompareAnnotations

The name of the stack to use as background to the annotations.

setBackground(ProviderAsStack) - Method in class ColoredBase

The background.

setBackgroundChannelIndex(int) - Method in class OutlinePreserveRelativeSize

Uses only this channel (identified by an index in the stack) as the background, -1 disables.

setBackgroundChannelProvider(ChannelProvider) - Method in class MorphologicalOperatorBase

setBackgroundColor(RGBColorBean) - Method in class PlotColorScheme

setBackgroundID(String) - Method in class VisualizeOnBackground

setBackgroundStackMap(StringMap) - Method in class AnnotationBackground

If non-null, maps underlying stack-name to a background.

setBackgroundStackName(String) - Method in class SegmentIntoMarks

setBeanExtension(String) - Method in class QuickMultiDatasetExperiment

setBeanExtension(String) - Method in class QuickMultiDatasetStructuredExperiment

setBelowMinValue(double) - Method in class RangeCompareBase

Constant to return if outside the range (below the minimum allowed)

setBest(boolean) - Method in class VoxelizedMarksChangeReporter

setBigNeighborhood(boolean) - Method in class Dilate

setBigNeighborhood(boolean) - Method in class ConnectedComponentsFromMask

If true uses 8 neighborhood rather than 4 neighborhood etc.

setBigNeighborhood(boolean) - Method in class DecomposeIntoConnectedComponents

if true, uses 8 neighborhood instead of 4, and similarly in 3d

setBigNeighborhood(boolean) - Method in class Dilate

setBigNeighborhood(boolean) - Method in class TraverseOuterContourOnImage

setBinary(boolean) - Method in class ScaleImage

Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are ouputted.

setBinaryInputChannelID(String) - Method in class AddDistanceTransform

The ID of the binary input mask that determines the region of the Watershed.

setBinarySgmn(BinarySegmentation) - Method in class BinarySegmentByObject

setBirthRepeats(int) - Method in class KernelReplace

setBit0(boolean) - Method in class RegionMembership

setBit1(boolean) - Method in class RegionMembership

setBit2(boolean) - Method in class RegionMembership

setBit3(boolean) - Method in class RegionMembership

setBit4(boolean) - Method in class RegionMembership

setBit5(boolean) - Method in class RegionMembership

setBit6(boolean) - Method in class RegionMembership

setBit7(boolean) - Method in class RegionMembership

setBitsPerPixel(int) - Method in class ForceBitsPerPixel

setBlockSize(SizeXY) - Method in class HOGParameters

The block-size as per OpenCV implementation (identical default-size).

setBlockStride(SizeXY) - Method in class HOGParameters

The block-stride as per OpenCV implementation (identical default-size).

setBlue(int) - Method in class RGBColorBean

Sets the blue component value.

setBlue(int) - Method in class RGBColor

Sets the blue component value.

setBlue(ChannelProvider) - Method in class ThreeChannels

setBold(boolean) - Method in class TextStyle

Whether to bold the drawn text

setBorderWidth(int) - Method in class MontageSlices

Adds a border around each part of the montage

setBounds(BoundRotation) - Method in class RandomOrientation

setBridgeMatcher(ObjectMatcher) - Method in class Bridge

Used to match each input-object to an intermediary-object

setBundleSize(int) - Method in class ObjectSerializerPeriodicReporter

setBundleSize(int) - Method in class VoxelizedMarksChangeReporter

setBySlices(boolean) - Method in class ConnectedComponentsFromMask

setCacheSize(int) - Method in class RelationWithMatches

Size of feature evaluation cache for featureEvaluatorMatch

setCalculateLevel(CalculateLevel) - Method in class CalculateLevelOne

setCalculateLevel(CalculateLevel) - Method in class ThresholderGlobal

setCalculateLevel(CalculateLevel) - Method in class LevelPerObjectBase

Method to calculate the level for a particular object.

setCalculateLevel(CalculateLevel) - Method in class GreaterThanThreshold

Calculates the level for the threshold

setCalculateLevel(CalculateLevel) - Method in class LevelFromHistogram

setCalculateLevel(CalculateLevel) - Method in class ThresholdHistogram

setCalculateLevel(CalculateLevel) - Method in class CalculateLevelBase

setCalculateLevelElse(CalculateLevel) - Method in class CalculateLevelRelativeToThreshold

setCaseSensitive(boolean) - Method in class PatternSpan

Iff true, a case sensitive search is used to match patterns.

setCellDefault(ArrangeStackBean) - Method in class Tile

setCells(List<Cell>) - Method in class Tile

setCellSize(SizeXY) - Method in class HOGParameters

The cell-size as per OpenCV implementation (identical default-size).

setCenterPoint(Point3d) - Method in class FitResult

setChangeExisting(boolean) - Method in class ConvertBase

If true, the existing channel can be changed.

setChannel(ChannelProvider) - Method in class ChannelProviderUnary

setChannel(ChannelProvider) - Method in class ChannelFilter

setChannel(ChannelProvider) - Method in class FromChannel

The ChannelProvider to use for dimensions.

setChannel(ChannelProvider) - Method in class FromChannel

setChannel(ChannelProvider) - Method in class FromChannelBase

setChannel(ChannelProvider) - Method in class IntensityGreaterEqualThan

setChannel(ChannelProvider) - Method in class UnaryWithChannelBase

setChannel(ChannelProvider) - Method in class WithChannelBase

setChannel(ChannelProvider) - Method in class FromChannelOrMask

A channel that is provided to the stack.

setChannel1(ChannelProvider) - Method in class ChannelProviderBinary

setChannel1(ChannelProvider) - Method in class ChannelProviderTernary

setChannel2(ChannelProvider) - Method in class ChannelProviderBinary

setChannel2(ChannelProvider) - Method in class ChannelProviderTernary

setChannel3(ChannelProvider) - Method in class ChannelProviderTernary

setChannelAssignFrom(ChannelProvider) - Method in class AssignFromChannel

setChannelConversionStyle(ChannelConvertStyle) - Method in class ConvertImageFormat

To convert as RGB or independently or in another way.

setChannelConverter(ConvertChannelTo<T>) - Method in class Convert

setChannelConverter(ConvertChannelTo<?>) - Method in class ConvertImageFormat

Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)

setChannelElse(ChannelProvider) - Method in class IfParamEquals

setChannelFilter(ChannelFilter) - Method in class ConvertImageFormat

Optionally, includes only certain channels when converting.

setChannelFirst(int) - Method in class Difference

Index of first channel

setChannelGroupID(int) - Method in class RegularExpression

setChannelID(String) - Method in class AddEdgeFilters

The ID of the channel that provides the input to the filter

setChannelIfVoxelZero(ChannelProvider) - Method in class IfVoxelZero

If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead

setChannelIndex(int) - Method in class FromStack

setChannelIndex(int) - Method in class FromStackChannel

setChannelIndex(int) - Method in class One

setChannelIndex(int) - Method in class MultiInputManagerQuick

If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack

setChannelLookup(ChannelProvider) - Method in class NormalizeDifferenceToMedian

setChannelMap(ChannelMap) - Method in class NamedChannels

setChannelMask(String) - Method in class ExportImageHistograms

If defined, this is the name of channel used as a mask over the values which are fed into the histogram

setChannelName(String) - Method in class ChannelFilter

setChannelName(String) - Method in class SingleChannel

setChannelName(String) - Method in class ConvertNamedChannelsToStack

By default all channels are converted into a stack.

setChannelSecond(int) - Method in class Difference

Index of second channel

setChannelsExtra(List<ChannelProvider>) - Method in class ScoreVoxels

setChannelsPerByteArray(int) - Method in class ForceChannelsPerByteArray

setChannelThreshold(ChannelProvider) - Method in class ThresholdAgainstChannel

setCheck(CheckMark) - Method in class Not

setCheckMark(CheckMark) - Method in class FromObjects

setCheckMark(CheckMark) - Method in class Check

setCheckMark(CheckMark) - Method in class Check

setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class GroupFiles

Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.

setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class BinaryClassifierImageLabeller

setClearOutsideMask(boolean) - Method in class ThresholdAgainstChannel

setCol(int) - Method in class Cell

setCollapseFilename(boolean) - Method in class FilePathAppendBase

setColor(RGBColorBean) - Method in class FromSingle

The single color to repeat.

setColor(RGBColorBean) - Method in class AnnotationLabel

An optional color associated with the label when displayed via GUI

setColor(RGBColorBean) - Method in class ColoredMask

setColors(ColorScheme) - Method in class ColorSchemeUnary

The delegate that creates the color-list before subsequent processing.

setColors(List<RGBColorBean>) - Method in class FromList

The list of colors to specify.

setColors(ColorScheme) - Method in class ColoredBaseWithGenerator

Colors to use for drawing objects

setColorScheme(ColorScheme) - Method in class GenerateToMatchObjects

setColorsUnpaired(ColorScheme) - Method in class CompareAnnotations

setColorUnselectedObjects(RGBColorBean) - Method in class OutlinePreserveRelativeSize

Optionally outline the other (unselected for the thumbnail) objects in this particular color.

setColumnDefinition(ColumnDefinition) - Method in class ExportObjectsFromCSV

Column definition for the CSV files

setColumnGroup(String) - Method in class ColumnDefinition

Name of CSV column used to group results (the same values, are outputted together)

setColumnID(String) - Method in class ColumnDefinition

Name of CSV column with the file identifier

setColumns(int) - Method in class MontageSlices

How many columns to use in the montage, or 0 to guess an approximately square output

setColumnUniquePixel(String) - Method in class ColumnDefinition

Name of CSV column with X coordinate of point for the first Object

setCombine(CombineObjectsForFeatures<T>) - Method in class FromObjects

setCommand(String) - Method in class MorphologicalOperation

One of: open, close, fill, erode, dilate, skel, outline

setComparerLeft(ComparableSource) - Method in class AnnotationComparisonInputManager

setComparerRight(ComparableSource) - Method in class AnnotationComparisonInputManager

setCondition(DictionaryCondition) - Method in class IfParamEquals

setCondition(DictionaryCondition) - Method in class IfKeyValueCondition

setConstant(double) - Method in class MaxWithConstant

setContains(String) - Method in class DescriptiveNameContainsImageLabeller

setContains(String) - Method in class FilterDescriptiveName

A descriptive-name must contain (case-sensitive) this string.

setConvert(ConvertChannelToWithHistogram<T>) - Method in class ConvertWithHistogram

setConvexHull(boolean) - Method in class FitPointsFromObjects

If true, Reduces the set of points by applying a convex-hull operation

setCopyFilesNaming(CopyFilesNaming<NoSharedState>) - Method in class CopyFilesNamingOne

setCountThreshold(int) - Method in class SummarizerSplitMoreThan

If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.

setCov(boolean) - Method in class ObjectRadiusStandardDeviation

setCreateMark(CreateMarkFromPoints) - Method in class PointsFitter

setCreateShort(boolean) - Method in class ArrangeRaster

setCreateShort(boolean) - Method in class GenerateString

setCreateShort(boolean) - Method in class TileWithLabels

setCreateShort(boolean) - Method in class DistanceTransform3D

setCreateShort(boolean) - Method in class DistanceTransformForEachObject3D

setCreateShort(boolean) - Method in class CreateNew

If True creates an unsigned short-image

setCsvFilePath(DerivePath) - Method in class FilterCSVColumn

setCsvIgnoreZeros(boolean) - Method in class ExportImageHistograms

Iff true, bins with zero-counts are not written as a row in the CSV file.

setCurrentTemp(double) - Method in class Geometry

setCustomName(String) - Method in class Feature

An optional additional name that be associated with the feature (defaults to an empty string).

setDatasetName(String) - Method in class ExperimentResultsExperimentStructure

The name of the experiment including version suffix

setDatasetNameSubdirectory(boolean) - Method in class ExperimentResultsExperimentStructure

If true the datasetName is appended as a subdirectory e.g.

setDatasets(StringSet) - Method in class QuickMultiDatasetExperiment

setDatasets(StringSet) - Method in class QuickMultiDatasetStructuredExperiment

setDatasetSpecific(String) - Method in class QuickMultiDatasetExperiment

setDatasetSpecific(String) - Method in class QuickMultiDatasetStructuredExperiment

setDatasetSuffix(String) - Method in class FilePathAppendBase

A suffix appended to the dataset name extracted from the reg exp

setDatasetVersion(String) - Method in class ExperimentResultsExperimentStructure

A version-suffix appended to the dataset name extracted from the reg exp

setDay(boolean) - Method in class ExperimentIdentifierAuto

If true, the current day (yyyy.MM.dd) is included in the output

setDebug(boolean) - Method in class RootPath

If true this root is preferred, when executing a job in debugging mode.

setDebug(boolean) - Method in class ThresholdedFeature

setDebugModeParameters(Optional<DebugModeParameters>) - Method in class InputContextParameters

Parameters for debug-mode (only defined if we are in debug mode)

setDefaultBehaviourString(Optional<String>) - Method in class ExperimentExecutor

If present, a string is printed in the description if the default-experiment is used, otherwise ignored.

setDefaultColors(ColorScheme) - Method in class OutputWriteSettings

The default color-scheme used for outputs, if no other scheme is specified.

setDefaultStackReaderForMetadata(StackReader) - Method in class ConvertNamedChannels

Supplies to the imageMetadataReader to use, if no other reader is specified.

setDefine(Define) - Method in class MarkEvaluator

setDefine(Define) - Method in class DefineOutputter

setDefine(DefineOutputter) - Method in class Develop

Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.

setDefine(DefineOutputter) - Method in class ExportReportFeaturesFromMulti

setDefine(DefineOutputterWithEnergy) - Method in class FromObjects

setDefine(DefineOutputter) - Method in class ExportObjectsAsCroppedImages

setDefine(DefineOutputterWithEnergy) - Method in class SegmentWithMarkedPointProcess

Adds definitions of stacks/objects etc.

setDelaySizeAtEnd(int) - Method in class MovieFromSlices

setDelegate(ResolvedBound) - Method in class BoundMinMax

setDelimiter(String) - Method in class DirectoryWithPrefix

Added between prefix and the filename, if the filename is defined.

setDelimiter(String) - Method in class SubsetRangeIfRequested

Character used to split the name into groups.

setDelimiter(String) - Method in class LastDirectoryAsPrefix

setDelta(double) - Method in class Mser

setDeltat(double) - Method in class AnisotropicDiffusion

the integration constant for the numerical integration scheme.

setDepth(double) - Method in class ImposeResolution

Physical pixel size of a voxel in z-dimension.

setDerivePath(DerivePath) - Method in class DualMarksAnnotationAsObjects

setDerivePath(DerivePath) - Method in class MarksAsObjects

setDerivePath(DerivePath) - Method in class MaskAsObject

Where to find the Mask to compare, as a function of the source file-path.

setDerivePath(DerivePath) - Method in class Objects

Where to find the objects to compare, as a function of the source file-path.

setDerivePath(DerivePath) - Method in class CollapseFileName

setDerivePath(DerivePath) - Method in class RemoveTrailingDirectory

setDictionary(DictionaryProvider) - Method in class FeatureEvaluator

Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.

setDictionary(DictionaryProvider) - Method in class EnergySchemeCreatorByElement

setDictionary(DictionaryProvider) - Method in class ScaleByDictionary

setDictionary(DictionaryProvider) - Method in class AssignFromDictionary

The dictionary from which an assignment will occur.

setDictionary(DictionaryProvider) - Method in class ScoreVoxels

setDictionary(DictionaryProvider) - Method in class DictionaryCondition

The dictionary to provide a value to check.

setDictionary(DictionaryProvider) - Method in class IfParamEqual

setDictionary(String) - Method in class ParamFromCollection

The name of the Dictionary that will be retrieved from SharedObjects.

setDictionary(DictionaryProvider) - Method in class FeatureListProviderLDAClassifier

setDictionary(DictionaryProvider) - Method in class FeatureValueCheckMark

setDictionary(DictionaryProvider) - Method in class DefineOutputterWithEnergy

setDictionary(DictionaryProvider) - Method in class GaussianSampler

The dictionary that parameterizes the Gaussian-distribution that is sampled from.

setDictionary(String) - Method in class Develop

If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.

setDictionary(DictionaryProvider) - Method in class SegmentMarksFromImage

If non-empty, a dictionary that is passed to the segmentation procedure.

setDimensions(DimensionsProvider) - Method in class ReportFeatureForMarks

setDimensions(DimensionsProvider) - Method in class FromDimensionsBase

setDimensions(DimensionsProvider) - Method in class FromDimensionsBase

setDimensions(DimensionsProvider) - Method in class RepeatSlice

Dimensions to create new mask

setDimensions(DimensionsProvider) - Method in class MergeBase

setDimensions(DimensionsProvider) - Method in class WithDimensionsBase

setDimensions(DimensionsProvider) - Method in class WithOptionalDimensionsBase

setDimensions(DimensionsProvider) - Method in class ToDimensions

The dimensions the source image/entity is desired to be scaled to.

setDimensions(DimensionsProvider) - Method in class FromMarks

setDimensions(DimensionsProvider) - Method in class RequireFeatureRelationThreshold

setDimensions(DimensionsProvider) - Method in class PointsFitterToMark

setDimensionsSourceFallback(DimensionsProvider) - Method in class ToDimensions

Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).

setDirection(DirectionVectorBean) - Method in class ConvertToPhysicalDistance

Direction of the distance being converted, defaults to a unit vector along the X-axis

setDirection(VectorInDirection) - Method in class FeatureMarkDirection

setDirectionVector(VectorInDirection) - Method in class FromUnitValueDistance

setDirectory(String) - Method in class FilesProviderWithDirectoryString

A directory in which to look for files.

setDirectory(Path) - Method in class DirectoryWithPrefix

setDirectory(String) - Method in class HomeSubdirectory

A relative-path (to the user home directory) which is used as an output directory

setDirectoryDataset(String) - Method in class QuickMultiDatasetExperiment

setDirectoryDistance(int) - Method in class QuickMultiDatasetStructuredExperiment

How many directories to recurse back from the current file to the Experiments/ directory

setDirectoryOutput(String) - Method in class QuickExperiment

setDisableDebugMode(boolean) - Method in class RootedFilePath

setDisableDebugMode(boolean) - Method in class Rooted

setDistance(int) - Method in class LevelPerObjectNeighbors

How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)

setDistanceMapProvider(ChannelProvider) - Method in class MergeSpatialClusters

A distance map which can also be used for making decisions on merging

setDistanceMax(double) - Method in class CalculateLevel

setDistanceTransformMultiplyBy(float) - Method in class AddDistanceTransform

Multiplies the distance transform by this factor to make it more meaningful in a short.

setDistanceTransformSmoothSigmaMeters(double) - Method in class AddDistanceTransform

If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below.

setDistanceX(double) - Method in class ReflectInAxesWithinDistance

setDistanceY(double) - Method in class ReflectInAxesWithinDistance

setDistanceZ(double) - Method in class ReflectInAxesWithinDistance

setDistanceZEndIfEmpty(UnitValueDistance) - Method in class XYOrientationExtendToZ

setDivideByZeroValue(double) - Method in class Divide

setDivisor(double) - Method in class PermutePropertySequenceDouble

What to divide the integer-sequence by.

setDo3D(boolean) - Method in class AnisotropicDiffusion

Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.

setDo3D(boolean) - Method in class ObjectCollectionProviderMorphological

setDo3D(boolean) - Method in class MorphologicalIterations

Whether to perform the morphological dimensions in 3D or 2D

setDo3D(boolean) - Method in class PairNeighbors

setDo3D(boolean) - Method in class TouchingVoxels

setDo3D(boolean) - Method in class Erode

setDo3D(boolean) - Method in class NumberRemovedVoxelsAfterClosing

setDo3D(boolean) - Method in class OutlineKernelBase

setDo3D(boolean) - Method in class UniformRandomRadiiProposer

setDrawReverseLine(boolean) - Method in class Orientation

setDuplicate(boolean) - Method in class Reference

If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate

setDuplicate(boolean) - Method in class Reference

If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate

setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class EnergySchemeCreatorByElement

setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class EnergySchemeCreatorByElement

setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class EnergySchemeCreatorByElement

setEmptyValue(double) - Method in class CenterOfGravity

setEmptyValue(double) - Method in class Intersection

setEmptyValue(double) - Method in class ArbitraryInsidePoint

setEmptyValue(int) - Method in class IntensityMeanMaxSlice

setEmptyValue(double) - Method in class IntensityMeanShellBase

setEmptyValue(double) - Method in class DerivedObject

setEnd(int) - Method in class SequenceInteger

An index beyond which we cannot iterate (inclusive).

setEnd(int) - Method in class IncrementingIntegers

setEnergyChannelIndex(int) - Method in class Identity

setEnergyChannelIndex(int) - Method in class RejectIfIntensityLessThan

setEnergyChannelIndex(int) - Method in class SingleChannel

setEnergyChannelIndex(int) - Method in class QuantileAcrossConnectedComponents

setEnergyChannelIndexCheck(int) - Method in class IdentityImposeValueRelationToHistogram

setEnergyChannelIndexFail(int) - Method in class IdentityImposeValueRelationToHistogram

setEnergyIndex(int) - Method in class NumberNeighboringVoxels

Index of which channel in the energy-stack to select

setEnergyIndex(int) - Method in class SpecificEnergyChannelBase

Index of which channel in the energy-stack to select

setEnergyIndex(int) - Method in class FeatureEnergyChannel

Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)

setEnergyIndex(int) - Method in class OutsideRange

setEnergyIndex(int) - Method in class Intensity

The channel that that forms the histogram

setEnergyIndex(int) - Method in class AsObjectMask

The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions

setEnergyIndex(int) - Method in class OverlapMaskBase

setEnergyIndexGradient(int) - Method in class TextureScore

setEnergyIndexMask(int) - Method in class IntensityMeanShellBase

A channel of the energyStack that is used as an additional mask using default byte values for on and off.

setEnergyIndexMask(int) - Method in class Intensity

Optionally, index of another channel that masks the histogram.

setEnergyIndexX(int) - Method in class IntensityGradientBase

setEnergyIndexY(int) - Method in class IntensityGradientBase

setEnergyIndexZ(int) - Method in class IntensityGradientBase

setEnergySchemeCreator(EnergySchemeCreator) - Method in class MarkEvaluator

setEnergySchemeCreator(EnergySchemeCreator) - Method in class SegmentWithMarkedPointProcess

Creates an energy scheme that assigns an energy score to each collection of marks.

setEnergyStack(EnergyStack) - Method in class FeatureInputEnergy

Assigns an EnergyStack to be associated with the input.

setEnergyStack(Optional<EnergyStack>) - Method in class FeatureInputEnergy

Assigns an optional EnergyStack to be associated with the input.

setEnergyTotal(double) - Method in class MarksWithTotalEnergy

The pre-annealed total energy

setEnergyTotal(double) - Method in class EnergySavedInd

setEquals(String) - Method in class FilterDescriptiveName

A descriptive-name must be exactly equal to (case-sensitive) this string.

setErodeAtBoundary(boolean) - Method in class ConvexHullBase

setError(int, Exception) - Method in class ResultsVector

Set an error state at a particular position.

setErrorAll(Exception) - Method in class ResultsVector

Set an error state at all positions.

setErrorDisconnectedObjects(boolean) - Method in class RemoveIntersectingVoxels

If true, throws an error if there is a disconnected object after the erosion

setErrorTree(DefaultTreeModel) - Method in class ProposerFailureDescription

setExactDepth(int) - Method in class DirectoryDepth

setExceptionIfEmpty(boolean) - Method in class FeatureHistogramStatistic

If true, then an exception is thrown if the histogram is empty, otherwise is returned.

setExcludeZero(boolean) - Method in class Intensity

Iff true, zero-valued voxels are excluded from the histogram

setExcludeZero(boolean) - Method in class IntensityMeanMaxSlice

setExcludeZero(boolean) - Method in class Intensity

If true, zeros are excluded from considering in the histogram

setExecutionTime(long) - Method in class OptimizationStep

setExitBeforeOptimization(boolean) - Method in class SegmentWithMarkedPointProcess

Iff true the algorithm exits before optimization begins (useful for debugging).

setExitWithMinima(boolean) - Method in class WatershedYeong

If true, exits early and just returns the minima, without any further segmentation

setExpandLabelZ(boolean) - Method in class TileWithLabels

setExperiment(RootedExperiment) - Method in class ExperimentResultsExperimentStructure

setExperiment(RootedExperiment) - Method in class ExperimentStructure

setExperimentIdentifier(ExperimentIdentifier) - Method in class OutputExperiment

A name for the experiment.

setExperimentType(String) - Method in class FilePathAppendBase

A folder identifying the type of experiment (where the outputs are all put in the same directory

setExperimentType(String) - Method in class QuickMultiDatasetStructuredExperiment

The value of $1 (see comment above) in naming-structure.

setExperimentType(String) - Method in class RootedExperiment

A directory identifying the type of experiment.

setExpression(String) - Method in class RegExSimple

A Java-style regular expression containing groups.

setExpression(String) - Method in class MatchRegularExpression

setExpression(String) - Method in class RegularExpression

setExtendInZ(boolean) - Method in class ExportObjectsAsCroppedImages

Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)

setExtension(String) - Method in class OneOrThreeChannelsWriter

setExtension(String) - Method in class AppendStack

setExtension(String) - Method in class AppendStackDirect

setExtensions(StringSet) - Method in class MatchExtensions

A set of file-extensions (without the period), one of which must match the end of a path.

setExtensions(StringSet) - Method in class BranchExtension

Any extensions to match (case insensitive) not including any leading period.

setExtractScoreSize(ExtractScoreSize<S>) - Method in class DirectAssignMode

setExtractScoreSize(ExtractScoreSize<S>) - Method in class UniformProposal

setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class TransformationAssignMode

setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class TransformationAssignMode

setExtractWeight(ExtractWeightFromMark) - Method in class KernelInitialMarksFromPartition

setExtraLength(int) - Method in class Midpoint

setFactor(double) - Method in class ScoreObjects

setFactor(double) - Method in class Scale

setFactorHigh(double) - Method in class Identity

setFactorLow(double) - Method in class Identity

setFactorStandardDeviation(double) - Method in class GaussianSampler

Multiples the standard deviation of the distribution found in keyStandardDeviation.

setFallback(FilesProvider) - Method in class SpecificPathList

If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown

setFallback(ScaleCalculator) - Method in class ToSuggested

Used as a delegate to calculate the scale if suggestedResize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).

setFallback(ChannelConvertStyle) - Method in class RGB

If a channel doesn't match an RGB pattern, this conversion-style can be used instead.

setFallback(ImageMetadataReader) - Method in class InferFromHeader

Fallback to use if EXIF information is non-existing or absent.

setFallbackName(String) - Method in class ExperimentIdentifierAuto

If there's no task-name, then this constant is used as a fallback name

setFeature(Feature<T>) - Method in class FeatureProviderDefine

The feature to provide.

setFeature(Feature<T>) - Method in class FeatureEvaluator

The single feature that will be calculated (possibly repeatedly) in the session.

setFeature(FeatureListEvaluator<FeatureInputSingleObject>) - Method in class OutputFeatureTable

A list of features to calculate in an evaluation context.

setFeature(Feature<FeatureInputSingleObject>) - Method in class ScoreObjects

Feature that calculates the score for an object.

setFeature(Feature<T>) - Method in class PermuteFeatureBase

setFeature(Feature<FeatureInputPairMemo>) - Method in class AddCriteriaFeatureRelationThreshold

setFeature(FeatureProvider<T>) - Method in class FeatureValueCheckMark

setFeature(FeatureProvider<FeatureInputMark>) - Method in class RequireFeatureRelationThreshold

setFeatureCondition(Feature<T>) - Method in class IfCondition

setFeatureCondition(Feature<T>) - Method in class IfConditionWithinRange

Calculates value for the condition - which is checked if it lies within a certain range

setFeatureElse(Feature<T>) - Method in class IfCondition

setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MultipleComparer

Calculates the cost used when making assignments.

setFeatureEvaluator(FeatureEvaluator<T>) - Method in class ReportFeatureEvaluator

setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class FeatureCostAssigner

setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class DiscardOutliers

setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches

setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ThresholdedFeature

setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ObjectCollectionProviderWithFeature

setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeGreedyToIncreaseObjectFeature

setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeToIncreaseObjectFeature

setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches

setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MergePairs

setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class MergePairs

Allows merge only if the feature-value satisfies a relation to this threshold

setFeatureProvider(FeatureProvider<T>) - Method in class FeatureEvaluator

The single feature that will be calculated (possibly repeatedly) in the session

setFeatures(List<FeatureProvider<T>>) - Method in class FeatureListEvaluator

A list of providers, combined together to form a list of features, to be calculated in a session

setFeatures(List<NamedBean<FeatureListProvider>>) - Method in class ExportFeatures

The features to be exported (after possibly some manipulation or augmentation).

setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class SegmentInstanceWithModel

Features to calculate for objects in the features output.

setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class ExportFeatures

Features applied to each group to aggregate values (accepting FeatureInputResults).

setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class PairNeighbors

Additional features that only depend on the image, so do not need to be replicated for every object.

setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class PairNeighbors

Additional features that are processed on the pair of images (i.e.

setFeatureTables(List<OutputFeatureTable>) - Method in class Develop

Specifies a feature-table that can also be outputted.

setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class FeedbackReceiverRequireArguments

setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class SegmentWithMarkedPointProcess

Processes feedback from the segmentation algorithm for outputting / debugging.

setFileFilter(String) - Method in class ExperimentResultsExperimentStructure

Files to search for

setFileFilterAndDirectory(Path) - Method in class SearchDirectory

Sets both the directory and the glob from a string containing both.

setFileId(String) - Method in class AppendCsv

Unique identifier for the stack, object-mask-collection etc.

setFileId(String) - Method in class FilePathBaseAppendToManagerWithFileID

Unique identifier for the stack, object-mask-collection etc.

setFileInput(NamedFiles) - Method in class GroupFiles

setFileInput(InputManager<FileInput>) - Method in class NamedChannels

setFileInput(InputManager<FileInput>) - Method in class Stacks

setFileInput(String) - Method in class QuickExperiment

A string indicating the input file(s)

setFileName(String) - Method in class ReportFeatureForManifestFileBase

setFilePath(String) - Method in class SortedSetSlice

setFilePath(String) - Method in class FromSerializedMarks

setFilePath(String) - Method in class FromSerializedObject

setFilePathParser(FilePathParser) - Method in class MultiFileReader

setFilePathProviderSVM(FilePathProvider) - Method in class FeatureListProviderSVMClassifier

setFilePrefix(String) - Method in class MovieFromSlices

setFiles(FilesProvider) - Method in class ReadFromFile

Provides a single file containing a dictionary.

setFiles(FilesProvider) - Method in class FilesProviderUnary

setFiles(FilesProviderWithDirectory) - Method in class FilesProviderWithDirectoryUnary

setFiles(FilesProvider) - Method in class FromFiles

A provider that should return exactly one File whose path is employed.

setFiles(FilesProviderWithDirectory) - Method in class Rooted

setFiles(FilesProvider) - Method in class NamedFiles

The files to use as inputs.

setFiles(FilesProviderWithDirectory) - Method in class NamedFilesWithDirectory

The files to use as inputs.

setFiles(FilesProviderWithDirectory) - Method in class QuickBase

A path to the main channel of each file

setFilter(ObjectFilter) - Method in class IfObjectFilter

setFilter(ObjectFilter) - Method in class ObjectCollectionProviderFilterBase

setFilter(ObjectFilter) - Method in class Filter

setFilter(ImageLabeller<T>) - Method in class ImageLabellerStringMap

setFilterFilesCsv(MatchedAppendCsv) - Method in class QuickBase

If set, a CSV is read with two columns: the names of images and a

setFindMaxima(boolean) - Method in class ExtractSlice

If true, the maxima of the score is searched for.

setFindOutlinePixelAngle(FindPointOnContour) - Method in class TraversePointsOnContour

setFirst(StringSet) - Method in class OutputEnableRulesSpecify

Output-names in the first-level.

setFirst(boolean) - Method in class AsSingle

Iff true, first object is used, otherwise the second

setFirst(StateTransformerBean<S, U>) - Method in class Compose

First transformation from S to U

setFirstLineHeaders(boolean) - Method in class CombineCSV

setFixRandomSeed(boolean) - Method in class SegmentWithMarkedPointProcess

Iff true uses a constant seed for the random-number-generator (useful for debugging).

setFlatten(boolean) - Method in class MultipleComparer

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

setFlatten(boolean) - Method in class CompareAnnotations

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

setFlatten(boolean) - Method in class ExteriorContour

If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D

setFlatten(boolean) - Method in class ColoredBase

If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced.

setFontColor(RGBColorBean) - Method in class TextStyle

Font-color of drawn text

setFontName(String) - Method in class TextStyle

Font-name of drawn text

setFontSize(int) - Method in class TextStyle

Font-size of drawn text

setForceChangeBytes(boolean) - Method in class Invert

If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.

setForceDetailedLogging(boolean) - Method in class OutputExperiment

Whether more detailed log-messages around each experiment occur.

setForceEagerEvaluation(boolean) - Method in class NamedChannelsAppend

setForceReader(String) - Method in class BioformatsReader

If non-empty forces usage of a particular bioformats plugin.

setForceRGB(boolean) - Method in class ArrangeRaster

If set, ensures every stack is converted into 3 channels

setFormats(List<HeaderFormat>) - Method in class InferFromHeader

The formats whose headers will be searched, to find sufficient metadata to populate ImageMetadata.

setForwardDirectionOnly(boolean) - Method in class XYOrientationExtendToZ

setFrom3i(ObjectMask) - Static method in class PointsFromObject

A sorted-set of three-dimensional integer points from the entire object-mask

setFromContour(ObjectMask) - Static method in class PointsFromObject

A set of points from the contour of object in three dimensions.

setGaussian(boolean) - Method in class AddEdgeFilters

If true, the Gaussian filter is included

setGaussianSigmaMeters(double) - Method in class AddEdgeFilters

setGeneratorList(List<RasterGenerator<T>>) - Method in class CombineRasterGenerator

setGlob(String) - Method in class MatchGlob

The string describing a glob e.g.

setGradient(ChannelProvider) - Method in class ScoreVoxels

setGraphColorScheme(PlotColorScheme) - Method in class PlotIndexBase

setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class MinimaImpositionGrayscaleReconstruction

setGreen(int) - Method in class RGBColorBean

Sets the green component value.

setGreen(int) - Method in class RGBColor

Sets the green component value.

setGreen(ChannelProvider) - Method in class ThreeChannels

setGroup(String) - Method in class AnnotationLabel

Specifies a group for the label (similar labels that are displayed together)

setGroup(DerivePath) - Method in class ExportFeatures

If non-null, this file-path is used to determine the group of the file.

setGroup(DerivePath) - Method in class GroupedStackBase

If defined, translates a file-path into a group.

setGroup(String) - Method in class CSVRow

setGroup(String) - Method in class AppendHistogram

setGroupNum(int) - Method in class RootFilePathRegEx

setHeight(int) - Method in class SizeXY

Size in Y dimension.

setHeight(double) - Method in class ImposeResolution

Physical pixel size of a voxel in y-dimension.

setHighestTwoRadiiOnly(boolean) - Method in class RadiiRatio

setHistogram(HistogramProvider) - Method in class HistogramProviderUnary

setHistogram(HistogramProvider) - Method in class ConvertWithHistogram

If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).

setHistogram(HistogramProvider) - Method in class SegmentChannel

An optional histogram of voxel intensity values which can be used by segment

setHistogram(HistogramProvider) - Method in class PlotHistogram

The histogram to plot.

setHistogram(HistogramProvider) - Method in class FromHistogram

If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.

setHistogramChannelIndex(int) - Method in class CalculateLevelBase

setHistogramIndex(int) - Method in class IdentityImposeValueRelationToHistogram

setHistogramsExtra(List<HistogramProvider>) - Method in class ScoreVoxels

setHorizontalAlign(String) - Method in class Overlay

setId(String) - Method in class DictionaryProviderReference

Unique identifier for the Dictionary to retrieve.

setId(String) - Method in class Reference

The identifier that uniquely determines the other feature to reference.

setId(String) - Method in class FeatureProviderReference

The name of the feature to reference.

setId(String) - Method in class FeatureResultsStatistic

The name of the feature, whose results will provide the statistic.

setId(String) - Method in class BinarySegmentationReference

setId(String) - Method in class FilePathProviderReference

setId(int) - Method in class Mark

setId(String) - Method in class Reference

setId(String) - Method in class FromChannel

An shared-objects identifier for a ChannelProvider to use for dimensions.

setId(String) - Method in class Reference

setId(String) - Method in class Reference

setId(String) - Method in class Reference

setId(String) - Method in class ReferenceOrElse

setId(String) - Method in class Reference

setId(String) - Method in class FeatureIntersectingObjects

ID for the particular object-collection

setId(DerivePath) - Method in class ExportFeatures

Translates an input file name to a unique ID.

setId(String) - Method in class MarkBoundsReference

setId(String) - Method in class MarkProposerReference

setId(String) - Method in class MarkMergeProposerReference

setId(String) - Method in class MarkSplitProposerReference

setId(String) - Method in class Reference

setId(String) - Method in class ReferenceOrEmpty

setId(int) - Method in class CreateEllipse

setId(String) - Method in class CSVRow

setId(String) - Method in class Reference

setIdentifierSubrange(Optional<IndexRangeNegative>) - Method in class InputContextParameters

If defined, this indicates and specifies only a subset of the naming-elements to use.

setIdentifierSuffix(String) - Method in class QuickMultiDatasetExperiment

setIdentifierSuffix(String) - Method in class QuickMultiDatasetStructuredExperiment

setIdGenerator(DerivePath) - Method in class ExportObjectsFromCSV

setIgnoreAtThreshold(boolean) - Method in class OutlineKernelBase

setIgnoreCase(boolean) - Method in class FilePathPattern

if true, case is ignored in the pattern matching.

setIgnoreContains(String) - Method in class AnnotationBackground

If non-empty, to not display any stacks in backgroundStackMap whose name contains this string.

setIgnoreFileNotFoundAppend(boolean) - Method in class NamedChannelsAppend

setIgnoreFittingFailure(boolean) - Method in class FitPointsFromObjects

If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown

setIgnoreHidden(boolean) - Method in class SearchDirectory

If true, case is ignored in the pattern matching.

setIgnoreHidden(boolean) - Method in class FilePathPattern

Iff true, any hidden-path is not considered, and simply ignored

setIgnoreHigherSide(boolean) - Method in class GaussianCumulative

setIgnoreLowerSide(boolean) - Method in class GaussianCumulative

setIgnoreMissingChannel(boolean) - Method in class IndependentChannels

Iff true and we cannot find a channel in the file, we ignore it and carry on

setIgnoreNaN(boolean) - Method in class Sum

If true, we ignore any NaN values.

setIgnoreNoObjects(boolean) - Method in class SegmentInstanceWithModel

If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.

setIgnoreRangeAxisOutside(boolean) - Method in class LinePlot

setIgnoreZero(boolean) - Method in class RatioNonMode

setIgnoreZeros(boolean) - Method in class HistogramCSVGenerator

Iff true bins in the histogram with a zero count are not written

setIgnoreZIfNaN(boolean) - Method in class DistanceTransform3D

If the z-resolution is undefined, the z dimenion is ignored.

setImageLabeller(ImageLabeller<T>) - Method in class ImageAssignLabel

Maps a label to an image

setImageMetadataReader(ImageMetadataReader) - Method in class ConvertNamedChannels

How to read the ImageMetadata from the file-system.

setImgChannelMapCreator(ChannelMap) - Method in class GroupFiles

setIncludeBatchDimension(boolean) - Method in class SegmentObjectsFromONNXModel

If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size of 1), instead of the usual 3-dimensional tensor describing channel, height, width.

setIncludeDirectories(boolean) - Method in class DirectoryStructure

If false, the folders are ignored, and only the file-name is used in the output

setIncludeFeatureNames(boolean) - Method in class EnergySchemeCreatorByElement

If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features

setIncludeFileName(boolean) - Method in class AppendDictionary

setIncludeFirst(boolean) - Method in class PairNeighbors

Include features for the First-object of the pair

setIncludeMerged(boolean) - Method in class PairNeighbors

Include features for the Merged-object of the pair

setIncludeSecond(boolean) - Method in class PairNeighbors

Include features for the Second-object of the pair

setIncludeShell(boolean) - Method in class MaxOverlapRatio

setIncludeZ(boolean) - Method in class Outline

If true the outline is also applied in the z-dimension, otherwise this is ignored as possible boundary

setIncludeZ(boolean) - Method in class NotTouchingSceneBorder

setIncrement(int) - Method in class SequenceInteger

Size of step to use when incrementing.

setIndex(int) - Method in class ChannelEntry

setIndex(int) - Method in class KernelPointCursor

The index in the buffer that the kernel currently is focussed on.

setIndex(int) - Method in class AtIndex

setIndex(int) - Method in class SliceAt

Index in z-dimension of slice to extract

setIndex(int) - Method in class SpecificAxisBase

Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)

setIndex(int) - Method in class IndexedRegionBase

setIndex(int) - Method in class OrderedRadius

setIndex(int) - Method in class AsObject

setIndex(int) - Method in class HOGFeature

Which index to return from the HOG descriptor.

setIndex(int, double) - Method in class DirectionVector

Sets an element of the vector by the index of its position.

setIndexDay(int) - Method in class TimestampPattern

The index of the group in regularExpression that encodes the day, starting from 0 for the first group.

setIndexEnd(int) - Method in class ExtractSliceRange

Slice index to end extracting from (inclusive).

setIndexHours(int) - Method in class TimestampPattern

The index of the group in regularExpression that encodes the hours, starting from 0 for the first group.

setIndexMinutes(int) - Method in class TimestampPattern

The index of the group in regularExpression that encodes the minutes, starting from 0 for the first group.

setIndexMonth(int) - Method in class TimestampPattern

The index of the group in regularExpression that encodes the month, starting from 0 for the first group.

setIndexNonZero(int) - Method in class SelectSlicesWithIndexBase

setIndexSeconds(int) - Method in class TimestampPattern

The index of the group in regularExpression that encodes the seconds, starting from 0 for the first group.

setIndexStart(int) - Method in class ExtractSliceRange

Slice index to start extracting from (inclusive).

setIndexYear(int) - Method in class TimestampPattern

The index of the group in regularExpression that encodes the year, starting from 0 for the first group.

setInitContext(OptimizationContext) - Method in class FeedbackBeginParameters

setInitialKernel(Kernel<T, S>) - Method in class KernelProposer

setInnerCoreDistance(double) - Method in class Ellipsoid

setInput(InputManager<T>) - Method in class AnnotationInputManager

The inputs to be annotated.

setInput(InputManager<T>) - Method in class InputOutputExperiment

The input-manager to specify where/which/how necessary inputs for the experiment occur.

setInput(InputManager<T>) - Method in class InputManagerUnary

The delegate input-manager which will be circumstantially called by the current input-manager.

setInput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor

setInput(InputManager<? extends ProvidesStackInput>) - Method in class MultiInputManager

setInput(InputManager<T>) - Method in class AnnotationComparisonInputManager

setInput(InputManager<NamedChannelsInputPart>) - Method in class NamedChannelsAppend

setInput(InputManager<NamedChannelsInput>) - Method in class ConvertNamedChannelsToStack

setInput(MultiInputManager) - Method in class FromCSVInputManager

setInputDebug(InputManager<T>) - Method in class BranchIfDebug

If defined, this provides an input to the manager when in debug-mode, rather than than otherwise inputs.

setInputDirectory(Optional<Path>) - Method in class InputContextParameters

If defined, a directory which can be used by beans to find input.

setInputFilterExtensions(Set<String>) - Method in class InputContextParameters

A list of extensions that can be used filter inputs

setInputFilterGlob(String) - Method in class InputContextParameters

A glob that can be used by beans to filter input

setInputName(String) - Method in class MultiInputManager

setInputName(String) - Method in class SegmentObjectsFromONNXModel

The name of the input in the ONNX model.

setInputName(String) - Method in class QuickExperiment

setInputName(String) - Method in class MultiInputManagerQuick

setInputPaths(Optional<List<Path>>) - Method in class InputContextParameters

A list of paths referring to specific inputs

setInputPointShift(float) - Method in class ConicFitterBase

setIntensity(ChannelProvider) - Method in class ScoreVoxels

setIntensityProvider(Provider<Stack>) - Method in class GenerateString

setInterleaveChannels(boolean) - Method in class SegmentObjectsFromONNXModel

If true, the channels are placed as the final position of the tensor (**after** width/height) instead of **before** width/height.

setInterpolate(boolean) - Method in class AtScale

setInterpolator(InterpolatorBean) - Method in class ScaleXY

setInterpolator(InterpolatorBean) - Method in class OutlinePreserveRelativeSize

Interpolator used when scaling the background

setInterpolator(InterpolatorBean) - Method in class ScaleToSize

setInverse(boolean) - Method in class IntersectsWithContainer

setInverse(boolean) - Method in class IntensityMeanShellBase

Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).

setInverseMask(boolean) - Method in class IntensityMeanShellBase

If true, uses the inverse of the passed mask.

setInvert(boolean) - Method in class MaskAsObject

If true the Mask is inverted before conversion into an ObjectCollection.

setInvert(boolean) - Method in class FromObjects

setInvert(boolean) - Method in class FilterWithRegularExpression

Iff true, then a file is rejected if the regular-expression matches and vice-versa.

setInvertDecisionValue(boolean) - Method in class FeatureListProviderSVMClassifier

setItem(T) - Method in class NamedBean

The item that is to be named, the underlying bean.

setItem(Feature<T>) - Method in class DefineSingle

The sole feature that forms the list.

setItem(FeatureListProvider<FeatureInput>) - Method in class PrependName

Provides the features and names before any prepending.

setItem(Feature<S>) - Method in class FeatureUnary

setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureDeriveFromPair

setItem(ReportFeature<MarksInitialization>) - Method in class ReportFeatureWrapError

setItem(Feature<FeatureInputHistogram>) - Method in class ThresholdHistogram

setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class DeriveFromPair

setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class FeatureListProviderAggregatePair

For each feature in the list, a corresponding aggregate feature is created in the output list.

setItem(Feature<FeatureInputHistogram>) - Method in class Intensity

Feature to apply to the histogram

setItem(Feature<FeatureInputSingleObject>) - Method in class DerivedObject

setItem(Feature<FeatureInputPairObjects>) - Method in class FeatureIntersectingObjectsSingleElement

setItem(FeaturePairObjects) - Method in class PairedWithMask

setItem(VoxelScore) - Method in class RejectIfIntensityLessThan

setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared

setItem(Feature<FeatureInputHistogram>) - Method in class Intensity

Feature to apply to the histogram

setItem(Feature<FeatureInputSingleObject>) - Method in class AsObjectMask

setItem(Feature<FeatureInputSingleObject>) - Method in class QuantileAcrossConnectedComponents

setItem(DerivePath) - Method in class Rooted

setItem(Feature<FeatureInputSingleMemo>) - Method in class CoefficientOfVarianceFromAll

setItem(Feature<FeatureInputSingleMemo>) - Method in class MeanFromAll

setItem(Feature<FeatureInputHistogram>) - Method in class Intensity

Feature to apply to the histogram

setItem(Feature<FeatureInputSingleMemo>) - Method in class FeaturePairMemoOne

setItem1(Feature<T>) - Method in class FeatureBinary

Provides the first value for the binary-function.

setItem2(Feature<T>) - Method in class FeatureBinary

Provides the second value for the binary-function.

setItemMean(Feature<T>) - Method in class StatisticalBase

setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class FeatureAsIndividualProportionate

setItemStdDev(Feature<T>) - Method in class StatisticalBase

setIterations(int) - Method in class AnisotropicDiffusion

How many iterations to perform diffusion.

setIterations(int) - Method in class MorphologicalOperatorBase

setIterations(int) - Method in class ObjectCollectionProviderMorphological

setIterations(int) - Method in class Repeat

The maximum number of iterations.

setIterations(MorphologicalIterations) - Method in class Intersection

The number of dilations and erosions to apply to determine if two objects intersect

setIterations(MorphologicalIterations) - Method in class IntensityMeanShellBase

The number of dilations and erosions to apply and whether to do in the Z dimension.

setIterations(int) - Method in class Erode

setIterations(int) - Method in class NumberRemovedVoxelsAfterClosing

setIterations(MorphologicalIterations) - Method in class Shell

The number of dilations and erosions to apply and whether to do in the Z dimension

setIterations(int) - Method in class MorphologicalOperation

iterations for erode, dilate, open, close

setIterations(int) - Method in class UniformProposal

setIterations(int) - Method in class NumberIterationsBase

The number of iterations for which the number-of-marks must remain constant.

setIterationsDilation(int) - Method in class MorphologicalIterations

Number of times to perform morphological dilation

setIterationsErosion(int) - Method in class MorphologicalIterations

Number of times to perform morphological erosion

setJobNumber(int) - Method in class JobDescription

setJobShortName(String) - Method in class JobDescription

setKappa(double) - Method in class AnisotropicDiffusion

A parameter kappa associated with the diffusion functions.

setKeepEntireImage(boolean) - Method in class ExportObjectsAsCroppedImages

If true, rather than writing out a bounding-box around the object-mask, the entire image is written

setKeepExtremes(boolean) - Method in class Identity

setKeepProcessorsFree(int) - Method in class DebugDependentProcessor

How many processors to avoid using for the tasks.

setKeepProcessorsFree(int) - Method in class ParallelProcessor

How many processors to avoid using for the tasks.

setKeepZ(boolean) - Method in class ImposeResolution

Keep the z-resolution if it is already defined

setKernel(Kernel<T, S>) - Method in class WeightedKernel

setKernel(Kernel<T, S>) - Method in class KernelProposerOptionSingle

setKernelFactoryList(WeightedKernelList<?, ?>) - Method in class FeedbackBeginParameters

setKernelHalfWidth(int) - Method in class Median

Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)

setKernelNegative(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual

setKernelPositive(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual

setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess

Proposes kernel-changes during iterations of hte marked-point-processes.

setKernelStateBridge(KernelStateBridge<U, T>) - Method in class TransformationAssignMode

setKey(String) - Method in class AssignFromDictionary

The key of the value in the dictionary that will be assigned.

setKey(String) - Method in class DictionaryCondition

The key in the dictionary whose value is checked.

setKey(String) - Method in class IfParamEqual

setKey(String) - Method in class ParamFromCollection

The name of the key in the dictionary, whose corresponding value will be returned.

setKey(String) - Method in class FromDictionary

setKeyGroupID(int) - Method in class RegularExpression

setKeyLower(String) - Method in class ScaleByDictionary

setKeyMean(String) - Method in class GaussianSampler

The name of the key in the dictionary with the mean of the distribution.

setKeyPrefix(String) - Method in class FromDictionary

Prefix prepended to key

setKeyRequired(boolean) - Method in class RegularExpression

setKeyStandardDeviation(String) - Method in class GaussianSampler

The name of the key in the dictionary with the standard-deviation.

setKeySuffix(String) - Method in class FromDictionary

setKeyUpper(String) - Method in class ScaleByDictionary

setLabel(String) - Method in class StackProviderWithLabel

setLabel(boolean) - Method in class MontageSlices

If true a label is added beside every image showing the slice index

setLabels(List<AnnotationLabel>) - Method in class ImageLabelStrategy

setLevel(int) - Method in class Constant

setLine(String[]) - Method in class CSVRow

setList(List<DefineAdderBean>) - Method in class Concatenate

setList(List<RegEx>) - Method in class RegExList

The list of RegExes that are successively tried to be matched.

setList(List<StringMapItem>) - Method in class StringMap

A list of mappings between a single-items in the respective sets.

setList(List<LoggingDestination>) - Method in class ToMultiple

The list of loggers to log to

setList(List<Feature<T>>) - Method in class Define

The list that specifies features.

setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class DefinedNamed

A list of FeatureListProviders with an associated name.

setList(List<Feature<T>>) - Method in class FeatureList

The list of features.

setList(List<Feature<T>>) - Method in class FeatureFromList

Assigns the list of features to use.

setList(FeatureList<T>) - Method in class FeatureFromList

Assigns the list of features to use.

setList(List<Provider<Stack>>) - Method in class ArrangeRaster

setList(List<DrawObject>) - Method in class Combine

setList(List<StackProviderWithLabel>) - Method in class TileWithLabels

setList(List<RegionMembership>) - Method in class RegionMap

setList(List<AddCriteriaPair>) - Method in class AddCriteriaOr

setList(List<FeedbackReceiver<T>>) - Method in class FeedbackReceiverList

setList(List<TerminationCondition>) - Method in class TerminationConditionListOr

setList(List<ColorProvider>) - Method in class Concatenate

A list of ColorProvider to be concatenated.

setList(List<CalculateLevel>) - Method in class CalculateLevelListBase

setList(List<ObjectFilter>) - Method in class ObjectFilterCombine

A list of other filters from which the sub-classes implement filtering behaviour.

setList(List<ObjectCollectionProvider>) - Method in class Concatenate

setList(List<BinarySegmentation>) - Method in class Sequence

A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)

setList(List<ProviderAsStack>) - Method in class Concatenate

setList(List<NamedBean<FromStack>>) - Method in class SpecificAndRename

setList(List<ChannelEntry>) - Method in class FromEntries

setList(List<FilesProvider>) - Method in class Combine

setList(List<InputManager<T>>) - Method in class Concatenate

The list of InputManagers that will be concatenated.

setList(List<Summarizer<T>>) - Method in class SummarizerAggregate

setList(List<CheckMark>) - Method in class AndList

setList(List<VisitScheduler>) - Method in class VisitSchedulerAnd

setList(List<VisitScheduler>) - Method in class VisitSchedulerUniformSample

setList(List<MarkProposer>) - Method in class MarkProposerFromList

setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class ScoreObjects

setListAppend(List<NamedBean<DerivePath>>) - Method in class NamedChannelsAppend

setListAppend(List<FilePathBaseAppendToManager>) - Method in class MultiInputManagerQuick

Additional entities that are appended to the multi-input

setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class BinaryClassifierImageLabeller

setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class EnergySchemeCreatorByElement

setListPaths(StringList) - Method in class SpecificPathList

If specified, this forms the list of paths which is provided as input.

setListReportFeatures(List<ReportFeature>) - Method in class ExportReportFeatures

setListStackProvider(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages

The channels we extract the object-masks from - all assumed to be of same dimension

setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages

The channels we extract the object-masks from - all assumed to be of same dimension

setLocalized(boolean) - Method in class FilesProviderWithDirectoryString

setLog(LoggingDestination) - Method in class OnlyIf

The logger to use if conditions are fulfilled

setLogExperiment(LoggingDestination) - Method in class OutputExperiment

Where log messages that do not pertain to a specific job (input) appear.

setLogExperimentPath(String) - Method in class QuickMultiDatasetExperiment

Relative path to a logger for the experiment in gneeral

setLoggerTaskCreator(LoggingDestination) - Method in class ParametersExperiment

This is a means to create new log-reporters for each task.

setLogPath(boolean) - Method in class Rooted

if true, the pathIn and pathOut are logged.

setLogTask(LoggingDestination) - Method in class InputOutputExperiment

Where log messages that do pertain to a specific job (input) appear.

setLogTaskPath(String) - Method in class QuickMultiDatasetExperiment

Relative path to a logger for a specific task

setMainChannelIndex(int) - Method in class NamedChannelsQuick

Index of the mainChannel

setMainChannelName(String) - Method in class NamedChannelsQuick

The name of the channel provided by the rasters in file Provider

setManifestDescriptionFunction(String) - Method in class MarksGeneratorBase

setManifestDeserializer(ManifestDeserializer) - Method in class CoupledManifestsInputManager

setManifestExperimentInputFileSet(FilesProvider) - Method in class CoupledManifestsInputManager

setManifestFunction(String) - Method in class ObjectSerializerPeriodicReporter

setManifestFunction(String) - Method in class VoxelizedMarksChangeReporter

setManifestInputFileSet(FilesProvider) - Method in class CoupledManifestsInputManager

setMap(StringMap) - Method in class ImageLabellerStringMap

setMarkBounds(MarkBounds) - Method in class MarkBoundsDefine

setMarkBounds(MarkBounds) - Method in class SegmentThresholdAboveMinBound

setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class MarkProposerStrategy

A mark-evaluator that is added to the GUI to support this annotation

setMarkFactory(MarkWithIdentifierFactory) - Method in class MarkEvaluator

setMarkFactory(MarkWithIdentifierFactory) - Method in class SegmentWithMarkedPointProcess

Creates a new mark, before perhaps further manipulations by a kernel.

setMarkFactory(MarkFactory) - Method in class FitPointsFromObjects

setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class KernelSplit

setMarkProposer(String) - Method in class MarkProposerStrategy

Name of the MarkProposer to use.

setMarkProposer(MarkProposer) - Method in class FromMarkProposer

setMarkProposer(MarkProposer) - Method in class MergeMarkEllipse

setMarkProposer(MarkProposer) - Method in class KernelBirthAndKill

setMarkProposer(MarkProposer) - Method in class KernelExchange

setMarkProposer(MarkProposer) - Method in class KernelBirthVoxelized

setMarkProposerAdditionalBirth(MarkProposer) - Method in class KernelBirthAndKill

setMarkProvider(SingleMarkProvider) - Method in class CreateMarkFromPoints

setMarkProvider(SingleMarkProvider) - Method in class ReportFeatureOnMark

setMarkProvider(SingleMarkProvider) - Method in class FromSingleMark

setMarkProvider(Provider<Optional>) - Method in class RequireFeatureRelationThreshold

setMarks(MarkCollection) - Method in class MarksWithTotalEnergy

The marks

setMarks(MarkCollectionProvider) - Method in class ReportFeatureOnMarks

setMarks(MarkCollection) - Method in class MarksWithDisplayStack

setMarks(Point2d, Orientation) - Method in class Ellipse

setMarks(MarkCollectionProvider) - Method in class FromMarks

setMarks(MarkCollectionProvider) - Method in class ScaleXY

setMarks(MarkCollectionProvider) - Method in class RetrieveSingleMarkOnly

setMarks(MarkCollectionProvider) - Method in class ColoredMarks

setMarksColored(ColoredMarks) - Method in class ColoredMarksWithDisplayStack

setMarksExplicit(Point3d, Orientation, Point3d) - Method in class ConicBase

setMarksExplicit(Point3d, Orientation) - Method in class ConicBase

setMarksExplicit(Point3d) - Method in class ConicBase

setMarksExplicit(Point3d, Orientation, Point2d) - Method in class Ellipse

setMarksExplicit(Point3d) - Method in class Ellipse

setMarksExplicit(Point3d, Orientation) - Method in class Ellipse

setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipse

setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipsoid

setMarksExplicit(Point3d) - Method in class Ellipsoid

setMarksExplicit(Point3d, Orientation) - Method in class Ellipsoid

setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksFromPartition

setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksProposed

setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksVoxelized

setMask(Provider<Mask>) - Method in class MaskProviderUnary

setMask(MaskProvider) - Method in class FromMaskBase

setMask(MaskProvider) - Method in class UnaryWithMaskBase

setMask(MaskProvider) - Method in class ScoreVoxels

setMask(MaskProvider) - Method in class FromChannel

setMask(MaskProvider) - Method in class SegmentChannel

An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel

setMask(Provider<Mask>) - Method in class ConnectedComponentsFromMask

setMask(MaskProvider) - Method in class AndObjectsWithMasks

setMask(Provider<Mask>) - Method in class FromMask

setMask(MaskProvider) - Method in class SegmentChannel

setMask(MaskProvider) - Method in class ColoredMask

setMask(Provider<Mask>) - Method in class FromChannelOrMask

A mask that is provided to the stack.

setMask(MaskProvider) - Method in class PairedWithMask

setMask(MaskProvider) - Method in class MaskAsSingleObject

setMask(MaskProvider) - Method in class FillHoles

setMask(Provider<Mask>) - Method in class CheckMarkWithMask

setMask(Provider<Mask>) - Method in class FindPointOnContourWalk

setMask(Provider<Mask>) - Method in class XYOrientationExtendToZ

setMaskContour(Provider<Mask>) - Method in class TraverseOuterContourOnImage

setMaskElse(MaskProvider) - Method in class IfPredicateBase

Returned instead of mask if the predicate is not satisfied

setMaskFilled(Provider<Mask>) - Method in class TraverseOuterContourOnImage

setMaskFilled(Provider<Mask>) - Method in class XYOrientationExtendToZ

setMaskIndex(int) - Method in class SurfaceSizeMaskNonZero

setMaskValue(int) - Method in class ExportImageHistograms

What voxel value to read as "On" in the mask above.

setMaskValue(int) - Method in class OverlapMaskBase

setMatch(String) - Method in class FilterCSVColumn

setMatch(String) - Method in class MatchedAppendCsv

setMatcher(PathMatcher) - Method in class SearchDirectory

setMatcher(PathMatcher) - Method in class MatchExtensions

setMatcher(ObjectMatcher) - Method in class RelationWithMatches

setMatcher(ObjectMatcher) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection

setMatcher(ObjectMatcher) - Method in class Match

setMax(int) - Method in interface Progress

Assigns the maximum value of progress that is possible.

setMax(int) - Method in class ProgressConsole

setMax(int) - Method in class ProgressIgnore

setMax(int) - Method in class ProgressIncrement

Assigns the maximum value of progress that is possible.

setMax(double) - Method in class BoundMinMax

setMax(double) - Method in class ResolvedBound

setMax(int) - Method in class ScaleByMinMaxValue

setMax(int) - Method in class ClampHistogramMax

setMax(UnitValueAreaOrVolume) - Method in class UnitsWithinRange

Maximum-boundary for acceptable range

setMax(boolean) - Method in class IdentityImposeValueRelationToHistogram

setMax(int) - Method in class OutsideRange

setMax(double) - Method in class MaxOverlapRatio

setMax(double) - Method in class InvertedMax

setMax(Feature<T>) - Method in class CompareWithRangeFeature

Calculates maximally-allowed range boundary

setMax(double) - Method in class RangeCompareFromScalars

Boundary value indicating maximally-allowed range value

setMaxCost(double) - Method in class MultipleComparer

The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.

setMaxCost(double) - Method in class FeatureCostAssigner

setMaxDirectoryDepth(int) - Method in class SearchDirectory

If non-negative the max depth of directories.

setMaxDirectoryDepth(int) - Method in class ExperimentResultsExperimentStructure

setMaxDistance(UnitValueDistance) - Method in class MergeWithOptionalDistanceConstraint

An optional maximum distance

setMaxDistance(UnitValueDistance) - Method in class CostOverlapWithinMidpointDistance

setMaxDistance(UnitValueDistance) - Method in class FindPointOnContourWalk

setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class AddDistanceTransform

setMaxDistanceCOG(UnitValueDistance) - Method in class MergeSpatialClusters

The maximum distance allowed between center-of-gravities of objects

setMaxDistanceDeltaContour(double) - Method in class AddDistanceTransform

The maximum distance allowed between two seeds in terms of their values in the distance map

setMaxDistanceDeltaContour(double) - Method in class MergeSpatialClusters

The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.

setMaxDistanceProposer(ScalarProposer) - Method in class VisitSchedulerMaxDistanceAlongContour

setMaxDistanceZ(ScalarProposer) - Method in class XYOrientationExtendToZ

setMaximumNumberChannels(int) - Method in class IntensityMoments

An upper limit on the number of channels in the energy-stack for which we create features.

setMaxIter(int) - Method in class Repeat

setMaxIter(int) - Method in class Repeat

setMaxIter(int) - Method in class Repeat

setMaxIter(int) - Method in class RadiiProposerRepeat

setMaxNumberItems(int) - Method in class Limit

setMaxNumberItems(int) - Method in class Limit

setMaxNumberProcessors(int) - Method in class DebugDependentProcessor

An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.

setMaxNumberProcessors(int) - Method in class ParallelProcessor

Theoretical maximum number of (CPU) processors to use in parallel.

setMaxNumberProcessors(int) - Method in class QuickMultiDatasetExperiment

An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.

setMaxNumberProcessors(int) - Method in class QuickMultiDatasetStructuredExperiment

setMaxNumItems(int) - Method in class LimitWithDirectory

setMaxSize(long) - Method in class Mser

setMaxSplitGroups(int) - Method in class CompareAnnotations

setMaxValue(long) - Method in class ToByteScaleByMaxValue

Assigns the maximum-value that will be represented in the scaled-values.

setMaxVar(double) - Method in class Mser

setMaxVolume(UnitValueAreaOrVolume) - Method in class FillHoles

setMaxX(int) - Method in class Box

Maximum X coordinate inclusive.

setMaxY(int) - Method in class Box

Maximum Y coordinate inclusive.

setMaxZ(int) - Method in class Box

Maximum Z coordinate inclusive.

setMean(double) - Method in class MeanScale

The mean.

setMedian(boolean) - Method in class AddEdgeFilters

If true, the median filter is included

setMedianRadiusMeters(double) - Method in class AddEdgeFilters

setMerge(boolean) - Method in class CutBelowThreshold

setMergedPosTolerance(double) - Method in class MergeMarkEllipse

setMergeMarkProposer(MarkMergeProposer) - Method in class KernelMerge

setMessage(String) - Method in class ReportFeatureWrapError

setMessageNoInputs(String) - Method in class InputOutputExperiment

A message written to the logger if no inputs exist for the experiment, and it thus ends early.

setMethod(String) - Method in class AutoLocalThreshold

setMethod(String) - Method in class ThresholderAutoIJ

One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).

setMethod(CopyFilesMethod) - Method in class CopyFiles

How the copying occurs from source to destination file.

setMin(int) - Method in interface Progress

Assigns the minimum value of progress that is possible.

setMin(int) - Method in class ProgressConsole

setMin(int) - Method in class ProgressIgnore

setMin(int) - Method in class ProgressIncrement

Assigns the minimum value of progress that is possible.

setMin(double) - Method in class BoundMinMax

setMin(double) - Method in class ResolvedBound

setMin(int) - Method in class ScaleByMinMaxValue

setMin(UnitValueAreaOrVolume) - Method in class UnitsWithinRange

Minimum-boundary for acceptable range

setMin(int) - Method in class OutsideRange

setMin(double) - Method in class RadiiMinRatio

setMin(Feature<T>) - Method in class CompareWithRangeFeature

Calculates minimally-allowed range boundary

setMin(double) - Method in class RangeCompareFromScalars

Boundary value indicating minimally-allowed range value

setMinConfidence(double) - Method in class ThresholdConfidence

The minimum confidence of an element for its object-mask to be initially included for consideration (before merging).

setMinConfidence(float) - Method in class DecodeMaskRCNN

Only proposals outputted from the model with a score greater or equal to this threshold are considered.

setMinConfidence(double) - Method in class DecodeEAST

Proposed bounding boxes below this confidence interval are removed from consideration.

setMinDiff(double) - Method in class MeanIntensityDifference

setMinDifference(int) - Method in class Difference

A minimum difference, below which 0.0 is returned

setMinDifference(int) - Method in class DifferenceCalculateLevelStandardDeviation

setMinDiversity(double) - Method in class Mser

setMinimaImposition(MinimaImposition) - Method in class ImposeMinima

setMinimumBoundingBoxVolume(int) - Method in class FloodFillEachIntensityLevel

Only objects whose bounding-box volume is greater or equal to this threshold are included.

setMinimumPerCluster(int) - Method in class ClusterByTimestamp

The minimum number of files that must exist for a cluster.

setMinIntensity(int) - Method in class RejectIfIntensityLessThan

setMinIntensity(int) - Method in class ThresholderSimpleFillHoles2D

Intensity for thresholding

setMinIntensityValue(int) - Method in class MorphologicalOperatorBase

setMinMaskValue(float) - Method in class DecodeMaskRCNN

Only voxels with a value greater or equal to this threshold are considered as part of the mask.

setMinMaxIgnoreBeforeIndex(int) - Method in class LinePlot

setMinMaxValues(int, int) - Method in class ToByteScaleByMinMaxValue

Assigns the minimum- and maximum-values which existing values are scaled against.

setMinNumberObjects(int) - Method in class DiscardOutliers

setMinNumberPoints(int) - Method in class SplitContourAtSaddlePoints

If a contour has less than this number of points, we don't split it, and return it as-is

setMinNumberVoxels(int) - Method in class SplitIntoSquares

Only includes squares that have at least this number of voxels.

setMinNumberVoxels(int) - Method in class ConnectedComponentsFromBinarySegmentation

setMinNumberVoxels(int) - Method in class ThresholdConfidence

The minimum number of voxels that must exist in a connected-component to be included.

setMinNumPoints(int) - Method in class CreateMarkFromPoints

setMinNumPoints(int) - Method in class PointsFitterToMark

If an object has fewer points than before being fitted, we ignore

setMinNumSlices(int) - Method in class XYOrientationExtendToZ

setMinNumZSlices(int) - Method in class AtLeastZSlices

setMinOverlap(double) - Method in class CostOverlapWithinMidpointDistance

setMinRadius(double) - Method in class LinearLeastSquaresEllipseFitter

setMinRadius(double) - Method in class LinearLeastSquaresEllipsoidFitter

setMinRatio(double) - Method in class DiscardOutliers

setMinResolution(double) - Method in class MinimumXYResolution

setMinSize(long) - Method in class Mser

setMinVal(double) - Method in class FeatureValueCheckMark

setMinVolume(UnitValueAreaOrVolume) - Method in class ConnectedComponentsFromMask

setMinVolume(UnitValueVolume) - Method in class VolumeMin

setMinVolumeConnectedComponent(UnitValueVolume) - Method in class AddDistanceTransform

setMinX(int) - Method in class Box

Minimum X coordinate inclusive.

setMinY(int) - Method in class Box

Minimum Y coordinate inclusive.

setMinZ(int) - Method in class Box

Minimum Z coordinate inclusive.

setMip(boolean) - Method in class NumberVoxels

setMip(boolean) - Method in class SurfaceNumberVoxelsBase

setMip(boolean) - Method in class OverlapMIPBase

setModelBinaryPath(String) - Method in class SegmentObjectsFromTensorFlowModel

Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.

setModelPath(String) - Method in class SegmentObjectsFromONNXModel

Relative-path to the model file in ONNX form, relative to the models/ directory in the Anchor distribution.

setModelTextGraphPath(String) - Method in class SegmentObjectsFromTensorFlowModel

Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.

setMultipleComparer(MultipleComparer) - Method in class MarkProposerStrategy

setMultipleOf(int) - Method in class FitTo

The eventual width and height of the image must be a multiple of this number.

setMultiplyBy(float) - Method in class DistanceTransform3D

setName(String) - Method in class FromXMLList

The name of the file in the current working directory WITHOUT THE .xml EXTENSION

setName(String) - Method in class NamedBean

The name associated with item.

setName(String) - Method in class RootPath

The name of the root-path, which need not be unique in itself.

setName(String) - Method in interface NameValue

Assigns the associated name.

setName(String) - Method in class SimpleNameValue

setName(String) - Method in class ExperimentIdentifierConstant

setName(String) - Method in class ChannelEntry

setName(String) - Method in class Kernel

setName(String) - Method in class WeightedKernel

setName(String) - Method in class AdjacentFile

A name to describe the adjacent file

setName(String) - Method in class FilePathAppendBase

The name of the appended entity

setNameLeft(String) - Method in class AnnotationComparisonInputManager

setNamer(FileNamer) - Method in class GroupFiles

setNamer(FileNamer) - Method in class RemoveExtension

setNamer(FileNamer) - Method in class SubsetRangeIfRequested

The namer that is called to provide names that are subsetted.

setNamer(FileNamer) - Method in class NamedFilesBase

setNamer(FileNamer) - Method in class QuickBase

Assigns each input a unique compact name.

setNameRight(String) - Method in class AnnotationComparisonInputManager

setNaming(CopyFilesNaming<T>) - Method in class CopyFiles

How an output name (and path) is selected for an input file.

setNavigateHigherDirectories(int) - Method in class MultiFileReader

Search x number directories higher than file.

setNoBlack(boolean) - Method in class ThresholderAutoIJ

setNormalize(boolean) - Method in class Identity

setNormalize(boolean) - Method in class BoundingBoxZOverlapRatio

setNormalizeFeatures(boolean) - Method in class FeatureListProviderSVMClassifier

Normalize features

setNumberBins(int) - Method in class HOGParameters

The number of bins in each histogram for a cell.

setNumberChannels(int) - Method in class ForceNumberChannels

setNumberColors(int) - Method in class TiffTimeSeries

setNumberColumns(int) - Method in class Tile

The number of columns to use in the table produced when tiling.

setNumberColumns(int) - Method in class CSVReader.OpenedCSVFile

setNumberDecimalPlaces(int) - Method in class FeatureCostAssigner

setNumberDigits(int) - Method in class IncrementingNumber

Number of digits in the number, with leading zeros as necessary.

setNumberDilations(int) - Method in class LevelPerObjectIndependently

setNumberFrames(int) - Method in class ForceNumberFrames

setNumberGPUProcessors(int) - Method in class ParallelProcessor

How many GPU processors to use when this is possible as a substitute for a CPU processor

setNumberLevelsGrouping(int) - Method in class CompareAnnotations

setNumberLoopPoints(int) - Method in class SplitContourAtSaddlePoints

setNumberPoints(int) - Method in class LinePlot

setNumberRows(int) - Method in class Tile

The number of rows to use in the table produced when tiling.

setNumberSubdirectories(int) - Method in class LastDirectories

How many directories to include in the name.

setNumCols(int) - Method in class TileWithLabels

setNumMarks(int) - Method in class FromMarkProposer

setObjectMatcher(ObjectMatcher) - Method in class Bridge

Used to match each intermediary-object to a final-object

setObjects(Provider<ObjectCollection>) - Method in class ObjectCollectionProviderUnary

setObjects(ObjectCollectionProvider) - Method in class OutputFeatureTable

The objects for which features are calculated.

setObjects(ObjectCollectionProvider) - Method in class ReportFeatureOnObjectsBase

setObjects(ObjectCollectionProvider) - Method in class DistanceTransformForEachObject3D

setObjects(ObjectCollectionProvider) - Method in class LevelPerObjectBase

The objects for whom a level is calculated

setObjects(ObjectCollectionProvider) - Method in class UnaryWithObjectsBase

setObjects(ObjectCollectionProvider) - Method in class GenerateToMatchObjects

setObjects(ObjectCollectionProvider) - Method in class FromObjects

setObjects(ObjectCollectionProvider) - Method in class IntersectsWith

setObjects(ObjectCollectionProvider) - Method in class Always

setObjects(ObjectCollectionProvider) - Method in class Intersection

setObjects(ObjectCollectionProvider) - Method in class Permute

setObjects(ObjectCollectionProvider) - Method in class ColoredObjects

Objects to draw on a background

setObjects(ObjectCollectionProvider) - Method in class ObjectAggregationBase

setObjects(ObjectCollectionProvider) - Method in class FromObjects

setObjects(ObjectCollectionProvider) - Method in class ObjectAsPoints

setObjects(ObjectCollectionProvider) - Method in class IncludeRandomObjects

setObjects(ObjectCollectionProvider) - Method in class PointsFromObjects

setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class FromObjects

setObjects(ObjectCollectionProvider) - Method in class ExportObjectsBase

setObjects(ObjectCollectionProvider) - Method in class PointsFitterToMark

setObjects1(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise

First collection with items to be merged

setObjects2(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise

Second collection with items to be merged

setObjectsBlue(ObjectCollectionProvider) - Method in class ThreeColoredObjects

setObjectsContainer(ObjectCollectionProvider) - Method in class WithContainerBase

setObjectsElse(ObjectCollectionProvider) - Method in class ReferenceOrElse

setObjectsGreater(ObjectCollectionProvider) - Method in class GreaterIntersectionWith

setObjectsGreen(ObjectCollectionProvider) - Method in class ThreeColoredObjects

setObjectsGrouped(ObjectCollectionProvider) - Method in class FilterByGroup

setObjectsLesser(ObjectCollectionProvider) - Method in class GreaterIntersectionWith

setObjectsRed(ObjectCollectionProvider) - Method in class ThreeColoredObjects

setObjectsRejected(ObjectCollectionProvider) - Method in class ObjectCollectionProviderFilterBase

setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentChannel

setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentWithSeeds

setObjectsSource(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects

setObjectsSource(ObjectCollectionProvider) - Method in class SegmentWithSeeds

setObjectsSplitBy(ObjectCollectionProvider) - Method in class SplitByObjects

setObjectsTarget(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects

setOfConnectedComponentIDs() - Method in class EncodedVoxels

setOff(int, int, int) - Method in interface BinaryOnOffSetter

Assigns an off state to a voxel at a particular point.

setOff(Point3i) - Method in interface BinaryOnOffSetter

Assigns an off state to a voxel at a particular point.

setOn(int, int, int) - Method in interface BinaryOnOffSetter

Assigns an on state to a voxel at a particular point.

setOn(Point3i) - Method in interface BinaryOnOffSetter

Assigns an on state to a voxel at a particular point.

setOpenInDesktop(boolean) - Method in class ExperimentExecutor

Whether to open the output directory in the desktop GUI after execution (if supported on the O/S).

SetOperationFailedException - Exception in org.anchoranalysis.core.index

When a set operation fails for a particular key.

SetOperationFailedException(String) - Constructor for exception SetOperationFailedException

Creates with only a message.

SetOperationFailedException(Throwable) - Constructor for exception SetOperationFailedException

Creates with only a cause.

setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess

The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.

setOptionList(List<KernelProposerOption<T, S>>) - Method in class KernelProposer

setOptions(ReadOptions) - Method in class BioformatsReader

Options that influence how stack is read.

setOptions(ReadOptions) - Method in class ReadOptionsDelegate

setOrientationProposer(OrientationProposer) - Method in class OrientationAndRadiiProposer

setOrientationXYProposer(OrientationProposer) - Method in class XYOrientationExtendToZ

setOtherwise(FileNamer) - Method in class IfRelativeToDirectory

The namer to use if the relative-to-directory option is not selected.

setOutline(boolean) - Method in class ColoredBase

If true, an outline is drawn around the entries.

setOutlineAtBoundary(boolean) - Method in class ExteriorContour

setOutlineColor(RGBColorBean) - Method in class SegmentInstanceWithModel

The color of the outline.

setOutlinePixelsRetriever(TraverseOuterCounter) - Method in class TraversePointsOnContour

setOutlinePixelsRetrieverReverse(TraverseOuterCounter) - Method in class TraversePointsOnContour

setOutlineWidth(int) - Method in class BoundingBoxOutline

setOutlineWidth(int) - Method in class Outline

setOutlineWidth(int) - Method in class CompareAnnotations

How many pixels should the outline be around objects.

setOutlineWidth(int) - Method in class AtScale

setOutlineWidth(int) - Method in class ColoredBase

The width of the outline (only relevant if outline==true.

setOutlineWidth(int) - Method in class OutlinePreserveRelativeSize

The width of the outline.

setOutlineWidth(int) - Method in class SegmentInstanceWithModel

The width of the outline.

setOutlineWidth(int) - Method in class VisualizeOnBackground

setOutlineWidth(int) - Method in class ExportObjectsAsCroppedImages

setOutPath(String) - Method in class InsertRegExGroups

Constructs a path as an output, replacing $1, $2 etc.

setOutput(OutputManager) - Method in class OutputExperiment

The output-manager that specifies how/where/which elements occur duing outputting.

setOutput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor

setOutput(String) - Method in class QuickMultiDatasetExperiment

setOutputName(String) - Method in class ToTextFileBase

The name to use (without extension) for the text-file log

setOutputName(String) - Method in class OutputNameStyle

An identifier used in rules to determine if an output is enabled or not.

setOutputName(String) - Method in class PeriodicSubdirectoryReporter

setOutputName(String) - Method in class MinimalExecutionTimeStatsReporter

setOutputName(String) - Method in class VoxelizedMarksChangeReporter

setOutputNameStyle(IndexableOutputNameStyle) - Method in class FromOutputName

setOutputRGBOutline(StringSet) - Method in class ExportObjectsAsCroppedImages

setOutputRGBOutlineFlattened(StringSet) - Method in class ExportObjectsAsCroppedImages

setOutputsDisabled(StringSet) - Method in class SpecificDisabled

The names of the outputs that are disbled.

setOutputsEnabled(StringSet) - Method in class SpecificEnabled

The names of the outputs that are enabled.

setOutputsEnabled(OutputEnabledRules) - Method in class OutputManager

Which outputs are enabled or not enabled.

setOutputShort(boolean) - Method in class GradientBase

Iff true, outputs a short channel, otherwise byte channel

setOutputStackProvider(StackProvider) - Method in class ImageAssignLabel

If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.

setOutputWriteSettings(OutputWriteSettings) - Method in class OutputManager

General settings (default file extensions, colors etc.) for outtping files.

setOutputWriteSettings(OutputWriteSettings) - Method in class QuickExperiment

setOutside(double) - Method in class UnitsWithinRange

Returned as a constant if a value lies otside the range

setOutsideAtThreshold(boolean) - Method in class OutlineKernelBase

setOverlappingObjects(boolean) - Method in class OutlinePreserveRelativeSize

Whether objects may overlap or not when unscaled.

setOverlapRatioThreshold(double) - Method in class KernelBirthAndKill

setPadding(double) - Method in class TextStyle

Padding added around the text in both dimensions if a default size is inferred (ignored if an explicit size is specified )

setPadding(Padding) - Method in class DrawCroppedObjectsGenerator

setPadding(Padding) - Method in class ExportObjectsBase

Padding placed on each side of the outputted image (if it's within the image)

setPaddingXY(int) - Method in class Padding

Padding placed on each side of the outputted image (if it's within the image) in XY directions

setPaddingZ(int) - Method in class Padding

Padding placed on each side of the outputted image (if it's within the image) in Z direction

setPairAddCriteria(AddCriteriaPair) - Method in class EnergySchemeCreatorByElement

setPairCollection(RandomCollection<IdentifiablePair>) - Method in class KernelMerge

setPairTypeClass(Class<?>) - Method in class RandomCollectionWithAddCriteria

setParam(P) - Method in class BeanInitializer

Sets the current parameters used for propagation.

setParameters(Dictionary) - Method in class EnergyStack

The associated parameters.

setParameters(HOGParameters) - Method in class HOGDescriptor

Parameters used for calculating HOG

setParameters(HOGParameters) - Method in class HOGFeature

Parameters used for calculating HOG.

setParamPrefix(String) - Method in class PermuteFeatureSequenceInteger

setParamPrefixAppendNumber(boolean) - Method in class PermuteFirstSecondOrder

If true the constant is appended to the param prefix (a dot and a number)

setPath(String) - Method in class RootPath

A path on a file-system to the directory, that defines the root.

setPath(String) - Method in class SingleFile

setPath(String) - Method in class RootedFilePath

setPath(String) - Method in class StaticFilePath

setPathAnnotation(DerivePath) - Method in class SinglePathStrategy

Derives the path to the corresponding annotation files, given a path to the image to be annotated.

setPathDefaultMarks(DerivePath) - Method in class MarkProposerStrategy

setPathDictionary(DerivePath) - Method in class MarkProposerStrategy

setPathLabel(DerivePath) - Method in class ImageCSVLabeller

Path to a CSV label file (comma-separated, with header, no quotes)

setPathParser(FilePathParser) - Method in class GroupFiles

setPaths(StringSet) - Method in class FileSetFromStringSet

setPaths(List<DerivePath>) - Method in class FilterForExistingFiles

All files need to be present

setPenaltyValue(double) - Method in class MaxOverlapRatio

setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class FeedbackBeginParameters

setPermutation(PermuteProperty<S>) - Method in class PermuteFeature

A permutation to apply.

setPermutations(List<PermuteProperty<S>>) - Method in class PermuteFeature

A list of permutations to apply.

setPermuteProperty(PermuteProperty<?>) - Method in class Permute

setPermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger

setPhysical(boolean) - Method in class UnitConverter

setPlotBackgroundColor(RGBColorBean) - Method in class PlotColorScheme

setPlotGridlineColor(RGBColorBean) - Method in class PlotColorScheme

setPoint(Point3i, int) - Method in class EncodedVoxels

setPointConnectedComponentID(Point3i, int) - Method in class EncodedVoxels

setPointDirection(Point3i, int, int, int) - Method in class EncodedVoxels

setPoints(Point3i, Point3i) - Method in class LineSegment

setPoints(Point3d, Point3d) - Method in class LineSegment

setPointsFitter(PointsFitter) - Method in class CreateMarkFromPoints

setPointsFitter(String) - Method in class MarkProposerStrategy

Name of the PointsFitter to use.

setPointsFitter(PointsFitter) - Method in class FitPoints

setPointsFitter(PointsFitterToMark) - Method in class FitPointsFromObjects

setPointsFitter(PointsFitter) - Method in class PointsFitterToMark

setPointsFitter(PointsFitter) - Method in class ReflectInAxesWithinDistance

setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class MergeLists

setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class XYOrientationExtendToZ

setPointsProposer(PointsProposer) - Method in class FitPoints

setPosition(Point3d) - Method in class MarkWithPosition

setPositionProposer(PositionProposer) - Method in class Position

setPositionProposer(PositionProposer) - Method in class Repeat

setPower(double) - Method in class MeanRaisedToPower

setPrefix(String) - Method in class DefineAdderWithPrefixBean

A prefix that is placed before the name of every bean created.

setPrefix(boolean) - Method in class FromXMLList

If true, a prefix is prepended to the name of each added bean.

setPrefix(String) - Method in class PrependName

The string to prepend to the custom-name of each feature.

setPrefix(String) - Method in class PathPrefixerAvoidResolve

A string prefixed to each output-path.

setPrefix(String) - Method in class DirectoryWithPrefix

Always prepended to outputted filenames.

setPrefix(String) - Method in class DeriveFromPair

setPrefix(String) - Method in class FeatureListProviderAggregatePair

The string to prepend.

setPrefix(String) - Method in class ExperimentStructure

setPrefixer(PathPrefixer) - Method in class OutputManager

Determines a prefix to use when outputting a file based upon an input-path.

setPrefixer(PathPrefixerAvoidResolve) - Method in class LastDirectoryAsPrefix

setPrefixer(PathPrefixerAvoidResolve) - Method in class Rooted

setPrefixerElse(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested

Called if the requested condition is not true.

setPrefixerIf(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested

Called if the requested condition is true.

setPrefixToRemove(String) - Method in class DirectoryStructure

setPrependColor(RGBColorBean) - Method in class Prepend

The color to prepend.

setPreserveAspectRatio(boolean) - Method in class FitTo

If true, the aspect-ratio is preserved between width and height.

setPreserveAspectRatio(boolean) - Method in class ToDimensions

If true, the ratio between x and y is kept constant when scaling.

setPreserveExtensionIfDuplicate(boolean) - Method in class RemoveExtension

Keeps the extension if the file-name (without the extension) becomes duplicated with another.

setPreserveSubdirectories(boolean) - Method in class ClusterByTimestamp

If true, the entire relative-path is used when copying files into the cluster directory.

setPrioritizeInputContext(boolean) - Method in class MatchExtensions

When true, any extensions available in the input-context are prioritized ahead of extensions.

setProbNeg(double) - Method in class KernelPosNeg

setProbPos(double) - Method in class KernelPosNeg

setProperty(String, T) - Method in class ObjectWithProperties

Assigns a value to a property with a particular name.

setPropertyPath(String) - Method in class PermuteProperty

Either a direct property of a bean or a nested-property with the children separated by full-stops.

setProposal(boolean) - Method in class VoxelizedMarksPeriodicReporter

setProposer(MarkFromCollectionProposer) - Method in class MarkFromCollectionProposerUnary

setProposer(MarkProposer) - Method in class MarkProposerUnary

setProvider(MarkCollectionProvider) - Method in class FromProvider

setPxlPartMemo(EnergyMemoList) - Method in class FeatureInputAllMemo

setPxlPartMemo(VoxelizedMarkMemo) - Method in class FeatureInputSingleMemo

setQuantile(double) - Method in class Quantile

The quantile.

setQuantile(double) - Method in class QuantileStretch

setQuantile(double) - Method in class Quantile

setQuantile(double) - Method in class DiscardOutliers

setQuantile(double) - Method in class Quantile

setQuantile(double) - Method in class QuantileAcrossObjects

setQuantile(double) - Method in class QuantileAcrossConnectedComponents

setQuantileHigh(double) - Method in class Range

setQuantileLow(double) - Method in class Range

setQuantileLower(double) - Method in class ToByteUpperLowerQuantileIntensity

setQuantileUpper(double) - Method in class ToByteUpperLowerQuantileIntensity

setRadiiProposer(RadiiProposer) - Method in class OrientationAndRadiiProposer

setRadiiProposer(RadiiProposer) - Method in class RadiiProposerRepeat

setRadius(double) - Method in class MarkWithPositionAndSingleRadius

setRadius(int) - Method in class AutoLocalThreshold

setRadius(double) - Method in class WithRadiusBase

setRadiusBound(Bound) - Method in class UniformRandomRadiiProposer

setRadiusInMeters(boolean) - Method in class WithRadiusBase

setRadiusX(double) - Method in class FitResult

setRadiusY(double) - Method in class FitResult

setRadiusZ(double) - Method in class FitResult

setRate(double) - Method in class Geometry

setReader(StackReaderOrientationCorrection) - Method in class RotateImageToMatchEXIFOrientation

Reads the image that is subsequently flattened.

setReaderMatching(StackReader) - Method in class BranchExtension

The reader to use if the extension matches.

setReaderNotMatching(StackReader) - Method in class BranchExtension

The reader to use if the extension does not match.

setReadFromResources(boolean) - Method in class SegmentObjectsFromONNXModel

When true, rather than reading modelPath from the file-system, it is read from Java resources on the class-path.

setReceive(MaskProvider) - Method in class CombineBase

setRecurseSubfolders(boolean) - Method in class MultiFileReader

setRecursive(boolean) - Method in class SearchDirectory

If true the search is applied recursively over sub-directories.

setRecursive(boolean) - Method in class ExperimentResultsExperimentStructure

Whether to apply the search recursively or not

setRed(int) - Method in class RGBColorBean

Sets the red component value.

setRed(int) - Method in class RGBColor

Sets the red component value.

setRed(ChannelProvider) - Method in class ThreeChannels

setReduce(FeatureFromList<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair

Method for reducing all pairs into a single value e.g.

setReferencePoissonIntensity(double) - Method in class MarkWithIdentifierFactory

setReferences(StringSet) - Method in class ReferencingFeatureListProvider

The names of other feature-lists, whose features may be referenced by this feature.

setReferencesFeatureListCreator(StringSet) - Method in class PermuteFeature

Makes sure a particular feature list creator is evaluated

setReferencesList(String) - Method in class FeatureProviderReference

The name of the list in which the feature referenced by id resides.

setRegex(String) - Method in class RegularExpressionBase

setRegEx(RegEx) - Method in class RegExMatcher

setRegEx(RegEx) - Method in class PathRegEx

Regular expression to use to match path with at least one group in it.

setRegEx(RegEx) - Method in class RemoveMatching

If a path matches a regular expression it is removed.

setRegEx(RegEx) - Method in class Exclude

A regular-expression to be matched against the identifiers of inputs.

setRegEx(RegEx) - Method in class InsertRegExGroups

The regular-expression to use for matching groups.

setRegEx(RegEx) - Method in class JoinRegExGroups

setRegex(String) - Method in class Replace

Regular expression to match against string

setRegex(String) - Method in class QuickBase

A regular-expression applied to the image file-path that matches three groups.

setRegEx(RegEx) - Method in class ExperimentStructure

setRegexAdjacent(String) - Method in class NamedChannelsQuick

This needs to be set if there is at least one adjacentChannel.

setRegExDir(String) - Method in class MultiFileReader

If non-empty a regular-expression is applied to directories.

setRegExFile(String) - Method in class MultiFileReader

If non-empty a regular-expression is applied to files.

setRegExString(String) - Method in class InsertRegExGroups

The regular-expression to use for matching groups, overloaded to handle legacy situations where a string is supplied.

setRegion(MarkRegion) - Method in class Thresholded

setRegion(MarkRegion) - Method in class Intensity

setRegionID(int) - Method in class VolumeMin

setRegionID(int) - Method in class FromMarks

setRegionID(int) - Method in class IndexedRegionBase

setRegionID(int) - Method in class ColoredMarks

setRegionID(int) - Method in class FeatureMarkRegion

setRegionID(int) - Method in class FeatureSingleMemoRegion

setRegionID(int) - Method in class FeaturePairMemoSingleRegion

setRegionID(int) - Method in class KernelBirthAndKill

setRegionMap(RegionMap) - Method in class EnergySchemeCreatorByElement

setRegionMap(RegionMap) - Method in class FromMarks

setRegionMap(RegionMap) - Method in class AsObject

setRegionMap(RegionMap) - Method in class SurfaceSizeMaskNonZero

setRegularExpression(String) - Method in class TimestampPattern

The regular-expression that checks a match and specifies groups for the encoded date-time.

setRejectIterationIfAllLow(boolean) - Method in class Erode

setRejectIterationIfDisconnected(boolean) - Method in class Erode

setRelation(RelationBean) - Method in class RelationToConstant

The relation to the threshold, where the threshold forms the second operand.

setRelation(RelationBean) - Method in class ObjectFilterRelation

setRelation(RelationBean) - Method in class MergePairs

Relation to threshold

setRelation(RelationBean) - Method in class IdentityImposeValueRelationToHistogram

setRelation(RelationToThreshold) - Method in class RejectIfConditionXYResolution

A predicate defined by the relationship of the XY-resolution to a constant threshold.

setRelation(RelationBean) - Method in class AddCriteriaFeatureRelationThreshold

setRelation(RelationBean) - Method in class RequireFeatureRelationThreshold

setRelativeForIdentifier(boolean) - Method in class InputContextParameters

If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.

setRemoveExtension(boolean) - Method in class FilePathPattern

if true, the extension is removed from paths before finding the pattern.

setRemoveExtensionInDescription(boolean) - Method in class LastDirectories

Whether to remove the file-extension from the filename.

setRemoveNaNColumns(boolean) - Method in class ExportFeaturesStyle

When true, columns containing all Double.NaN values are removed before outputting.

setRemoveTouchingBorderXY(boolean) - Method in class FeatureCostAssigner

setRepeat(int) - Method in class MovieFromSlices

setRepeats(int) - Method in class KernelBirth

Total number of births

setRepeatZProvider(Provider<Stack>) - Method in class GenerateString

Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider

setReplaceMatchesWithSolids(boolean) - Method in class CompareAnnotations

setReplacement(String) - Method in class SubstituteRegularExpression

setReplacement(String) - Method in class Replace

What to replace in the path

setReplacement(String) - Method in class AdjacentFile

The replacement string used to determine the file

setReplaceWithMidpoint(boolean) - Method in class MergeGreedyToIncreaseObjectFeature

setReportFitterErrors(boolean) - Method in class FitPoints

setRequireAllFilesMatch(boolean) - Method in class GroupFiles

setRequireArguments(RequireArguments) - Method in class OnlyIf

The conditions that must be fulfilled

setRequireArguments(RequireArguments) - Method in class FeedbackReceiverRequireArguments

setRequireBBoxNeighbors(boolean) - Method in class MergeWithFeature

Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch

setRequireTouching(boolean) - Method in class MergeWithFeature

Requires the object-masks to touch.

setResizeTo(SizeXY) - Method in class GroupedMeanChannelTask

If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)

setResizeTo(SizeXY) - Method in class HOGDescriptor

The input-image is rescaled to this width/height before calculating HOG descriptors

setResizeTo(SizeXY) - Method in class HOGFeature

The input is rescaled to this width/height before calculating HOG descriptors.

setRestrictTo(MaskProvider) - Method in class Invert

If set, the inversion only occurs on a particular region of the mask, as determined by this mask

setRewardHigherSide(boolean) - Method in class GaussianCumulative

Treat the higher side as if it's the the fill cdf

setRewardLowerSide(boolean) - Method in class GaussianCumulative

setRgb(boolean) - Method in class FromChannelOrMask

If true, the output contains three channels (the input and two duplicates) instead of one

setRoot1(double) - Method in class QuadraticEquationSolver.QuadraticRoots

The first root.

setRoot2(double) - Method in class QuadraticEquationSolver.QuadraticRoots

The second root.

setRootInStructure(boolean) - Method in class ExperimentResultsExperimentStructure

If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}

setRootName(String) - Method in class Rooted

The name of the root-path to associate with this fileset.

setRootName(String) - Method in class RootedFilePath

setRootName(String) - Method in class Rooted

setRootName(String) - Method in class Rooted

setRootName(String) - Method in class QuickBase

If non-empty then a rooted filesystem is used with this root

setRootName(String) - Method in class RootedExperiment

Root-name assuming multi-rooted structure.

setRootNameForStructure(String) - Method in class ExperimentResultsExperimentStructure

If rootInStructure==true, the rootName is placed in the folder structure.

setRootPath(Path) - Method in class RootDirectory

setRotationAngle(Bound) - Method in class BoundRotation2D

setRotationX(Bound) - Method in class BoundRotation3D

setRotationY(Bound) - Method in class BoundRotation3D

setRotationZ(Bound) - Method in class BoundRotation3D

setRotMatrix(DoubleMatrix2D) - Method in class FitResult

The rotation matrix, which must be considered immutable to be used here.

setRow(int) - Method in class Cell

setSampleEvery(int) - Method in class SampleWithDirectory

setScalarProposer(ScalarProposer) - Method in class MaxWithConstant

setScalarProposer(ScalarProposer) - Method in class Scale

setScale(double) - Method in class MeanScale

The scale, typically the standard-deviation.

setScale(double) - Method in class MontageSlices

Whether to increase or reduce the size of the images

setScaleCalculator(ScaleCalculator) - Method in class ScaleXY

setScaleCalculator(ScaleCalculator) - Method in class ScaleXY

Determines how much to scale by

setScaleCalculator(ScaleCalculator) - Method in class Scale

setScaleCalculator(ScaleCalculator) - Method in class AtScale

setScaleCalculator(ScaleCalculator) - Method in class Invert

The delegate ScaleCalculator whose calculation will be inverted.

setScaleCalculator(ScaleCalculator) - Method in class ScaleImage

Calculates what scale-factor to apply on the image.

setScaleCalculator(ScaleCalculator) - Method in class ScaleXY

setScaleFactor(double) - Method in class GradientBase

setScaleLabel(boolean) - Method in class TileWithLabels

setScaleLower(double) - Method in class ScaleByDictionary

setScaleLower(double) - Method in class ToByteUpperLowerQuantileIntensity

Sets the min by multiplying the quantileLower by this constant.

setScaleRadii(double) - Method in class ConicFitterBase

setScaleUpper(double) - Method in class ScaleByDictionary

setScaleUpper(double) - Method in class ToByteUpperLowerQuantileIntensity

Sets the max by multiplying the quantileUpper by this constant.

setScore(VoxelScore) - Method in class ScoreVoxels

setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class ExtractSlice

setSecond(boolean) - Method in class ExperimentIdentifierAuto

Only relevant if time==true.

setSecond(List<NamedBean<StringSet>>) - Method in class OutputEnableRulesSpecify

Output-names in the second-level (for all first level output-names)

setSecond(StateTransformerBean<U, T>) - Method in class Compose

Second transformation from U to T

setSecondary(boolean) - Method in class VoxelizedMarksPeriodicReporter

If proposal is true, this toggles between the primary and secondary proposal

setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class StateReporterToPixelized

setSegment(BinarySegmentation) - Method in class BinarySegmentationOne

setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary

setSegment(BinarySegmentation) - Method in class SegmentChannel

Segmentation algorithm

setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannel

setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelByObject

setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentStack

The segmentation procedure.

setSegment(SegmentChannelIntoObjects) - Method in class SegmentWithSeeds

setSegment(BinarySegmentation) - Method in class ConnectedComponentsFromBinarySegmentation

setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentInstanceWithModel

The segmentation algorithm.

setSegment(SegmentIntoMarks) - Method in class SegmentMarksFromImage

How to perform the segmentation.

setSegmentStack(BinarySegmentation) - Method in class SegmentOnMaximumIntensityAndExpandInZ

setSelect(String) - Method in class DeriveFromPair

Either "merged" or "first" or "second" indicating which feature to delegate from

setSelectChannels(FromStacks) - Method in class GroupedStackBase

Selects which channels are included, optionally renaming.

setSeperator(String) - Method in class CombineCSV

setSequence(SequenceInteger) - Method in class PermutePropertySequence

A sequence of integers, with each element assigned assigned directly during the permutation, or after further manipulation.

setSequence(OutputSequenceIndexed<T, S>) - Method in class ChangeableOutputSequence

setSeriesIndex(int) - Method in class FromStackReader

The series to open to the read the metadata (zero-indexed).

setSharedState(S) - Method in class SharedStateRememberConverted

The shared state.

setShell(double) - Method in class MarkEllipseFactory

setShell(double) - Method in class MarkEllipsoidFactory

setShell(double) - Method in class Ellipse

The size of the shell, expressed as a ratio of the radius.

setShell(double) - Method in class Ellipsoid

setShell(double) - Method in class FromObjects

setShell(double) - Method in class CreateEllipse

setShell(double) - Method in class ConicFitterBase

setShowAgg(boolean) - Method in class MemoryUsageReporter

setShowBest(boolean) - Method in class MemoryUsageReporter

setShowDomainAxis(boolean) - Method in class BarPlot

setShowOngoingJobsLessThan(int) - Method in class ParallelProcessor

When the number of ongoing jobs is less than this threshold, they are shown in event logs.

setShowVerticalAxisLines(boolean) - Method in class PlotInstance

setShuffle(boolean) - Method in class InputContextParameters

If true, the order of the inputs are shuffled (randomized).

setSigma(double) - Method in class BlurStrategy

setSigma(double) - Method in class GaussianBlur2D

setSigmaInMeters(boolean) - Method in class BlurStrategy

setSilentlyDeleteExisting(boolean) - Method in class OutputManager

Whether to silently first delete any existing output at the intended path, or rather throw an error.

setSimplePairCollectionID(String) - Method in class KernelMerge

setSize(SizeXY) - Method in class TextStyle

Explicit size of the image the string is draw on

setSize(double) - Method in class Aggregator

setSize(SizeXY) - Method in class PlotHistogram

Size of the image produced showing a plot of the histogram.

setSize(SizeXY) - Method in class OutlinePreserveRelativeSize

Size of all created thumbnails

setSize(SizeXY) - Method in class ScaleToSize

setSize(SizeXY) - Method in class MovieFromSlices

setSizeXY(SizeXY) - Method in class SpecifyDimensions

Length of X and Y dimensions.

setSizeZ(int) - Method in class SpecifyDimensions

Length of Z dimension.

setSkipAtBorder(boolean) - Method in class FillHoles

If true we do not fill any objects that touch the border

setSkipFileName(boolean) - Method in class LastDirectories

Iff true the filename is not considered, only the subdirectories.

setSkipFileName(boolean) - Method in class FilePathAppendBase

setSkipFirstTrim(int) - Method in class RemoveTrailingDirectory

setSkipFirstTrim(int) - Method in class FilePathAppendBase

setSkipMissingChannels(boolean) - Method in class NamedChannelsAppend

setSkipNumberSubdirectories(int) - Method in class LastDirectories

Initially skip this number of directories before including them in the description.

setSlice(ChannelProvider) - Method in class RepeatSlice

setSliceFirst(int) - Method in class MontageSlices

First slice.

setSliceID(int) - Method in class SelectSlicesBase

Index of slice to use, or -1 to use all slices

setSliceIndex(int) - Method in class RepeatSlice

Which slice to use from mask

setSliceLast(int) - Method in class MontageSlices

Last slice.

setSlicesSeparately(boolean) - Method in class FitBoxToOnVoxels

setSmoothingFactor(double) - Method in class SplitContourAtSaddlePoints

setSource(String) - Method in class StringMapItem

The origin of the mapping.

setSource(FeatureSource<T, S, U>) - Method in class ExportFeatures

Source of feature-values to be exported.

setSources(List<NamedBean<ComparableSource>>) - Method in class MultipleComparer

The other entities to compare with the annotation.

setSplitIdentifierRegex(String) - Method in class CompareAnnotations

If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.

setSplitProposer(MarkSplitProposer) - Method in class KernelSplit

setSquareSize(int) - Method in class SplitIntoSquares

setStack(Provider<Stack>) - Method in class StackProviderUnary

setStack(Provider<Stack>) - Method in class StackProviderWithLabel

setStack(DisplayStack) - Method in class ColoredMarksWithDisplayStack

setStack(DisplayStack) - Method in class MarksWithDisplayStack

setStack(ProviderAsStack) - Method in class FromStack

Provides a stack.

setStack(ProviderAsStack) - Method in class SegmentStack

The stack to segment

setStack(StackProvider) - Method in class ExportObjectsFromCSV

The stack that is the background for our objects

setStackAsChannel(boolean) - Method in class MultiInputManagerQuick

If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)

setStackBackground(boolean) - Method in class VisualizeOnBackground

setStackEnergy(Provider<Stack>) - Method in class FeatureEvaluator

Optionally specifies an energy-stack to be associated with every calculation input.

setStackEnergy(StackProvider) - Method in class FromImage

Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).

setStackEnergy(StackProvider) - Method in class BinaryClassifierImageLabeller

setStackEnergy(StackProvider) - Method in class ExtractSlice

setStackEnergy(StackProvider) - Method in class DefineOutputterWithEnergy

setStackID(String) - Method in class IfStackExists

setStackName(String) - Method in class One

If defined, processing only occurs the stack with this specific stack and index.

setStackNameDefault(String) - Method in class AnnotationBackground

The name of the default stack from backgroundStackMap to display as background when annotating.

setStackProviderID(String) - Method in class FromStack

Specifies the ID of an existing stack.

setStackProviderID(String) - Method in class FromStackChannel

setStackReader(StackReader) - Method in class AnnotatorStrategy

How to read raster Stacks from the file-system.

setStackReader(StackReader) - Method in class InputManagerWithStackReader

setStackReader(StackReader) - Method in class MaskAsObject

How to read the Mask from the file-system.

setStackReader(StackReader) - Method in class FromStackReader

The StackReader to use to read the image metadata.

setStackReader(StackReader) - Method in class FlattenAsChannel

Reads the image that is subsequently flattened.

setStackReader(StackReader) - Method in class ImposeResolution

Reads an image before a resolution is imposed.

setStackReader(StackReader) - Method in class MultiFileReader

setStackReader(StackReader) - Method in class ReadVoxelExtentXml

Reads an image before a resolution is imposed.

setStackReader(StackReader) - Method in class RejectIfConditionXYResolution

Reads an image before a resolution is imposed.

setStackReaderAdjacent(StackReader) - Method in class NamedChannelsQuick

The raster-reader to use for opening any adjacent-channels

setStackReaderAppend(StackReader) - Method in class QuickBase

The raster-reader for reading any appended files

setStart(int) - Method in class SequenceInteger

The index to begin iteration from.

setStartIndex(int) - Method in class MovieFromSlices

setStartingIntensity(int) - Method in class FloodFillEachIntensityLevel

The first intensity-value to consider as a valid object (e.g.

setStateReporter(StateReporter<T, S>) - Method in class TransformationAssignMode

setStrategy(BlurStrategy) - Method in class Blur

setStringRasterGenerator(TextStyle) - Method in class GenerateString

setStrongEdgeEnhancer(boolean) - Method in class AnisotropicDiffusion

If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.

setStyle(ExportFeaturesStyle) - Method in class ExportFeatures

Visual style for how feature export occurs.

setStyle(ExportFeaturesStyle) - Method in class SegmentInstanceWithModel

Visual style for how feature export occurs.

setSubdirectory(String) - Method in class AppendDictionary

setSubdirectory(String) - Method in class ExperimentResultsExperimentStructure

If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/

setSubtractConstant(int) - Method in class IntensityGradientBase

setSubtractFromMaskOnly(boolean) - Method in class SubtractMean

setSubtractRadii(double) - Method in class ConicFitterBase

setSummarizer(Summarizer<S>) - Method in class SummarizerInputFromManager

setSummarizer(Summarizer<S>) - Method in class SummarizeBase

setSummarizerElse(Summarizer<T>) - Method in class SummarizerSplitMoreThan

Used for summary if count(elements) <= countThreshold

setSummarizerGreaterThan(Summarizer<T>) - Method in class SummarizerSplitMoreThan

Used for summary if count(elements) > countThreshold

setSuppress3D(boolean) - Method in class MorphologicalOperatorBase

setSuppress3D(boolean) - Method in class SurfaceNumberVoxelsBase

setSuppress3D(boolean) - Method in class SegmentThresholdAboveMinBound

setSuppressDirectories(boolean) - Method in class FromDescriptiveName

If true, any directory separators in the identifier in a descriptive-name are replaced by underscores.

setSuppressErrors(boolean) - Method in class ExportFeaturesStyle

When false, an image is reported as errored, if any exception is thrown during calculation.

setSuppressErrors(boolean) - Method in class FromObjects

When true, exceptions aren't thrown when feature-calculations fail, but rather a log error message is written.

setSuppressExceptions(boolean) - Method in class JobProcessor

setSuppressExceptions(boolean) - Method in class QuickMultiDatasetExperiment

setSuppressExceptions(boolean) - Method in class QuickMultiDatasetStructuredExperiment

setSuppressOutlineZ(boolean) - Method in class ColoredBase

if true, the outline is suppressed in the z-dimension i.e.

setSuppressRes(boolean) - Method in class RadiiRatio

setSuppressRootOut(boolean) - Method in class Rooted

if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.

setSuppressSeries(boolean) - Method in class ConvertImageFormat

If true, the series index is not included in the outputted file-names.

setSuppressSubfolders(boolean) - Method in class DefineOutputter

setSuppressZ(boolean) - Method in class BoundingBoxIntersection

setSuppressZ(boolean) - Method in class DistanceTransform3D

setSuppressZ(boolean) - Method in class DistanceTransformForEachObject3D

setSuppressZ(boolean) - Method in class MergeWithOptionalDistanceConstraint

setSuppressZ(boolean) - Method in class CostOverlapWithinMidpointDistance

setSuppressZ(boolean) - Method in class ImageMomentsBase

If true co-voariance is suprpessed in z-dimension

setSuppressZ(boolean) - Method in class CenterOnMask

setSuppressZ(boolean) - Method in class UniformRandom

setSuppressZ(boolean) - Method in class SurfaceSizeMaskNonZero

setSuppressZ(boolean) - Method in class EllipsoidBase

Iff true, surpresses covariance in the z-direction.

setSuppressZCovariance(boolean) - Method in class FromObjects

setSuppressZCovariance(boolean) - Method in class LinearLeastSquaresEllipsoidFitter

setTarget(String) - Method in class StringMapItem

The destination of the mapping.

setTargetSize(SizeXY) - Method in class FitTo

The target size.

setTask(Task<T, S>) - Method in class JobProcessor

setTask(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor

setTask(Task<U, S>) - Method in class ConvertNamedChannels

The underlying task that will be called, perhaps with a different input-type.

setTask(Task<MultiInput, S>) - Method in class QuickExperiment

setTask(Task<T, S>) - Method in class QuickMultiDatasetExperiment

setTask(Task<T, S>) - Method in class QuickMultiDatasetStructuredExperiment

setTaskProcessor(JobProcessor<T, S>) - Method in class InputOutputExperiment

What task is associated with the experiment, and how it is processed.

setTemperature(double) - Method in class OptimizationStep

setTemplateMark(MarkFactory) - Method in class MarkWithIdentifierFactory

setTermination(TerminationCondition) - Method in class SimulatedAnnealing

setText(String) - Method in class GenerateString

Text to draw on an image

setThreshold(double) - Method in class RelationToConstant

The constant threshold.

setThreshold(int) - Method in class CutBelowThreshold

setThreshold(int) - Method in class CalculateLevelRelativeToThreshold

setThreshold(UnitValueDistance) - Method in class IntensityGreaterEqualThan

setThreshold(double) - Method in class ThresholdedFeature

setThreshold(UnitValueVolume) - Method in class ThresholdedVolume

setThreshold(RelationToThreshold) - Method in class Count

setThreshold(RelationToThreshold) - Method in class RatioThreshold

setThreshold(double) - Method in class FeatureIntersectingObjectsThreshold

Only considers values greater or equal to the threshold

setThreshold(double) - Method in class AddCriteriaFeatureRelationThreshold

setThreshold(double) - Method in class RequireFeatureRelationThreshold

setThreshold(RelationToThreshold) - Method in class GreatestAreaSlice

setThreshold(RelationToThreshold) - Method in class Thresholded

setThreshold(RelationToThreshold) - Method in class IfCondition

setThresholder(Thresholder) - Method in class BinarySegmentationThreshold

setThresholder(Thresholder) - Method in class Threshold

The thresholder that will convert a channel into a binary-channel

setThresholdHours(double) - Method in class ClusterByTimestamp

Files whose creation-time differs <= this parameter are joined into the same cluster.

setThresholdNumberObjectsGlobal(int) - Method in class ThresholdConfidence

When the number of objects is greater or equal than this, they are reduced globally, without separation.

setThrowExceptionForInsufficientPoints(boolean) - Method in class CreateMarkFromPoints

setThumbnail(ThumbnailFromObjects) - Method in class CombineObjectsForFeatures

Generates a thumbnail representation of one or more combined objects, as form a single input.

setThumbnail(ThumbnailFromStack) - Method in class FromImage

Method to generate a thumbnail for images.

setTime(boolean) - Method in class ExperimentIdentifierAuto

If true, the current time (HH.mm.ss) is included in the output

setTimeIndex(int) - Method in class ConvertNamedChannelsToStack

setTimeIndexGroupID(int) - Method in class RegularExpression

setTimes(int) - Method in class Repeat

How many times to duplicate the list.

setTimestampPatterns(List<TimestampPattern>) - Method in class ClusterByTimestamp

The patterns which can be used to extract a date-time from a filename.

setTimeZoneOffset(int) - Method in class ClusterByTimestamp

If >= 0, sets a specific time-offset in hours.

setTitle(String) - Method in class ReportFeatureEvaluator

setTitle(String) - Method in class ReportFeatureForManifestFileBase

setTolerance(int) - Method in class UnchangedScore

An exponent of 10 which determines a tolerance, less than which a score will be deemed unchanged compared to another.

setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class RemovePartitionAndThen

setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class VoxelizeWithTransform

setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class KernelStateBridgePixelize

setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class KernelStateBridgeTransformer

setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class AddDualTransformer

setTransformerPrimary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer

setTransformerSecondary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer

setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class KernelStateBridgeTransformer

setTransposed(boolean) - Method in class CombineCSV

setTrimTrailingDirectory(int) - Method in class RemoveTrailingDirectory

setTrimTrailingDirectory(int) - Method in class FilePathAppendBase

setUniqueLabel(String) - Method in class AnnotationLabel

Label that uniquely identifies the ID (for machine purposes)

setUnit(UnitConverter) - Method in class BoundingBoxExtent

setUnit(UnitConverter) - Method in class FeatureSingleMemoRegion

setUnitType(String) - Method in class DistancePhysical

setUnitType(String) - Method in class AreaPhysical

setUnitType(String) - Method in class VolumePhysical

setUnitType(String) - Method in class FeatureConvertUnits

setUnitType(String) - Method in class UnitConverter

setUnitTypeFrom(String) - Method in class ConvertUnits

setUnitTypeTo(String) - Method in class ConvertUnits

setUnitValueDistance(UnitValueDistance) - Method in class FromUnitValueDistance

setupBefore(Dimensions, ImageFileEncoding) - Method in class ConvertTo

Always called before any batch of calls to ConvertTo.convertSliceOfSingleChannel(java.nio.ByteBuffer, int, org.anchoranalysis.image.core.dimensions.OrientationChange).

setupBefore(Dimensions, ImageFileEncoding) - Method in class FloatFromUnsignedByte

setupDictionary(Dictionary) - Method in class FromDictionaryBase

setUseLastSeriesIndexOnly(boolean) - Method in class NamedChannels

setUseLastSeriesIndexOnly(boolean) - Method in class Stacks

setUseMax(boolean) - Method in class OverlapRatio

setUseMax(boolean) - Method in class OverlapRatioMask

setUserFriendlyLabel(String) - Method in class AnnotationLabel

Descriptive user-friendly label displayed via GUI

setUseZ(boolean) - Method in class RemoveTouchingBorder

setUseZ(boolean) - Method in class TraverseOuterContourOnImage

setValue(T) - Method in class NamedBean

setValue(T) - Method in interface NameValue

Assigns the associated value.

setValue(V) - Method in class SimpleNameValue

setValue(double) - Method in class Constant

The constant value.

setValue(double) - Method in class DistancePhysical

setValue(double) - Method in class DistanceVoxels

setValue(double) - Method in class UnitValueArea

setValue(double) - Method in class VolumePhysical

setValue(double) - Method in class VolumeVoxels

setValue(double) - Method in class AssignValue

setValue(int) - Method in class CreateNew

setValue(double) - Method in class UnaryWithValueBase

setValue(String) - Method in class DictionaryCondition

The value the key should have in the dictionary, in order for the condition to be fulfilled.

setValue(int) - Method in class EmptyHistogramConstant

setValue(String) - Method in class IfParamEqual

setValue(double) - Method in class ConstantScaleFactor

setValue(int) - Method in class CountEqual

setValue(double) - Method in class IdentityImposeValueRelationToHistogram

setValue(double) - Method in class NormalizeByConstant

setValue(String) - Method in class Constant

setValue(double) - Method in class Constant

setValue(double) - Method in class WithValueBase

setValueByDimension(int, double) - Method in class Tuple3d

Assigns a value to a component of the tuple corresponding to a particular dimension by index.

setValueByDimension(int, float) - Method in class Tuple3f

Assigns a value to a component of a tuple corresponding to a particular dimension by index.

setValueIfEmpty(double) - Method in class FeatureHistogramStatistic

The value to return iff exceptionifEmpty is false.

setValueIfTooFewVoxels(double) - Method in class ImageMomentsBase

A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments

setValueNoObject(int) - Method in class ScoreObjects

setValueNoObjects(double) - Method in class FeatureIntersectingObjects

setValues(DoubleSet) - Method in class PermutePropertyDoubleSet

The respect double values to assign during the permutation.

setValues(StringSet) - Method in class PermutePropertyStringSet

The respect string values to assign during the permutation.

setVaryColors(boolean) - Method in class SegmentInstanceWithModel

If true the colors change for different objects in the image (using a default color set).

setVersion(String) - Method in class ExperimentIdentifierConstant

setVerticalAlign(String) - Method in class Overlay

setVisitScheduler(VisitScheduler) - Method in class TraverseOuterContourOnImage

setVisuallyShortenDecimals(boolean) - Method in class ExportFeaturesStyle

When true, feature-values are shown as visually compressed as possible, including suppressing decimal places.

setWeight(double) - Method in class KernelProposerOptionSingle

setWeightBackground(double) - Method in class OtsuWeighted

setWeightForeground(double) - Method in class OtsuWeighted

setWeightItem1Greater(double) - Method in class Range

setWeightItem2Greater(double) - Method in class Range

setWeightNegative(double) - Method in class KernelProposerOptionDual

setWeightPositive(double) - Method in class KernelProposerOptionDual

setWeightWidthDescription(int) - Method in class ImageLabelStrategy

setWhenBinaryChannel(StackWriter) - Method in class BranchChannels

Writer employed if a stack is a single-channeled binary image.

setWhenDetailed(LoggingDestination) - Method in class SwitchDetailedLogging

Logger to use when detailed-logging is on

setWhenEqual(ObjectCollectionProvider) - Method in class IfParamEqual

setWhenFalse(DrawObject) - Method in class IfElse

setWhenNot(LoggingDestination) - Method in class SwitchDetailedLogging

Logger to use when detailed-logging is off

setWhenNotEightBit(StackWriter) - Method in class BranchChannels

Writer employed if a stack contains channels that are not 8-bit.

setWhenNotEqual(ObjectCollectionProvider) - Method in class IfParamEqual

setWhenRelative(FileNamer) - Method in class IfRelativeToDirectory

The namer to use if the relative-to-directory option is selected.

setWhenRGB(StackWriter) - Method in class BranchChannels

Writer employed if a stack is a three-channeled RGB image.

setWhenRGBAlpha(StackWriter) - Method in class BranchChannels

Writer employed if a stack is a four-channeled RGBA image.

setWhenSingleChannel(StackWriter) - Method in class BranchChannels

Writer employed if a stack is a single-channeled image, not guaranteed to be binary.

setWhenThreeChannels(StackWriter) - Method in class BranchChannels

Writer employed if a stack is a three-channeled non-RGB image.

setWhenTrue(DrawObject) - Method in class IfElse

setWidth(int) - Method in class SizeXY

Size in X dimension.

setWidth(double) - Method in class Difference

Width (what the difference is divided by)

setWidth(double) - Method in class ImposeResolution

Physical pixel size of a voxel in x-dimension.

setWidthFactor(double) - Method in class DifferenceCalculateLevelStandardDeviation

setWindowSize(int) - Method in class CenterSliceWindow

setWindowSize(SizeXY) - Method in class HOGParameters

The window-size as per OpenCV implementation.

setWithin(double) - Method in class UnitsWithinRange

Returned as a constant if a value lies within the range

setWithinValue(double) - Method in class CompareWithRange

Constant to return if value lies within the range

setWithinValue(double) - Method in class CompareWithRangeFeature

Constant to return if value lies within the range

setWriter(DrawObject) - Method in class Flatten

setWriter(StackWriter) - Method in class BranchChannels

Default writer, if a more specific writer is not specified for a condition.

setWriter(StackWriter) - Method in class WriteResolutionXml

setWriterAlways2D(StackWriter) - Method in class BranchStack

Writer to use if it is guaranteed that the image will always be 2D.

setWriterElse(StackWriter) - Method in class BranchStack

Otherwise the writer to use.

setWriterIfNoSuggestion(StackWriter) - Method in class BranchSuggestedFormat

The writer to use if there is no suggested file-format.

setWriters(List<NamedBean<?>>) - Method in class OutputWriteSettings

Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)

setWritersIfSuggested(List<StackWriter>) - Method in class BranchSuggestedFormat

A list of writers to select if a given format is used

setX(double) - Method in class VectorInDirection

setX(String) - Method in class PlotAxisLabels

setX(int) - Method in class Point2i

X-axis component of point.

setX(int) - Method in class Tuple3d

X-axis component of the tuple.

setX(double) - Method in class Tuple3d

X-axis component of the tuple.

setX(int) - Method in class Tuple3i

X-axis component of the tuple.

setXDiv(double) - Method in class Orientation

setXY(String, String) - Method in class PlotAxisLabels

setY(double) - Method in class VectorInDirection

setY(String) - Method in class PlotAxisLabels

setY(int) - Method in class Point2i

Y-axis component of point.

setY(int) - Method in class Tuple3d

Y-axis component of the tuple.

setY(double) - Method in class Tuple3d

Y-axis component of the tuple.

setY(int) - Method in class Tuple3i

Y-axis component of the tuple.

setYAxisLowerMargin(double) - Method in class LinePlot

setYAxisMargins(double) - Method in class LinePlot

setYAxisUpperMargin(double) - Method in class LinePlot

setYValGetter(LinePlot.YValGetter<T>) - Method in class LinePlot

setZ(double) - Method in class VectorInDirection

setZ(int) - Method in class Tuple3d

Z-axis component of the tuple.

setZ(double) - Method in class Tuple3d

Z-axis component of the tuple.

setZ(int) - Method in class Tuple3i

Z-axis component of the tuple.

setZAlign(String) - Method in class Overlay

setZSliceGroupID(int) - Method in class RegularExpression

setZSliceNum(int) - Method in class SortedSetSlice

shallowCopy() - Method in class ColorList

Creates a new list, containing the same elements as the current list.

shallowCopy() - Method in class GraphWithPayload

Creates a new graph with identical elements and structure, reusing the existing vertice and edge data objects.

shallowCopy() - Method in class RandomCollectionWithAddCriteria

shallowCopy() - Method in class MarksWithEnergyBreakdown

shallowCopy() - Method in class MarksWithTotalEnergy

Make a shallow copy

shallowCopy() - Method in class VoxelizedMarksWithEnergy

Creates a shallow-copy of the marks

shallowCopy() - Method in class EnergySavedAll

shallowCopy() - Method in class EnergySavedInd

shallowCopy() - Method in class EnergySavedPairs

shallowCopy() - Method in class ColoredMarks

shallowCopy() - Method in class MarkCollection

shallowCopy() - Method in class OverlayCollection

shallowDuplicate() - Method in class FeatureList

Creates a new feature-list which contains identical elements.

ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape

ShapeRegularityCenterSlice() - Constructor for class ShapeRegularityCenterSlice

ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape

ShapeRegularityMIP() - Constructor for class ShapeRegularityMIP

SharedFeatures - Class in org.anchoranalysis.feature.shared

A group of features made available to other features to reference.

SharedFeatures() - Constructor for class SharedFeatures

Create empty, without any features.

SharedFeaturesSubset<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared

A subset of features from SharedFeatures that share a common feature input-type.

SharedFeaturesSubset(NameValueMap<Feature<T>>) - Constructor for class SharedFeaturesSubset

SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store

Objects shared between different components.

SharedObjects(CommonContext) - Constructor for class SharedObjects

sharedObjectsRequired() - Method in class FeatureInitialization

Retrieves the shared-objects associated with the initialization, or throws an an exception if they do not exist.

SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller

SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>, String, String) - Constructor for class SharedStateFilteredImageOutput

SharedStateRememberConverted - Class in org.anchoranalysis.plugin.mpp.experiment.shared

Shared-state that remembers converted inputs for corresponding unconverted inputs.

SharedStateRememberConverted() - Constructor for class SharedStateRememberConverted

SharedStateSegmentInstance<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.task.segment

Shared-state for instance segmentation

SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, String, FeatureExporterContext) - Constructor for class SharedStateSegmentInstance

SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.stack

SharedStateSelectedSlice(Outputter) - Constructor for class SharedStateSelectedSlice

Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological

Shell() - Constructor for class Shell

shift() - Method in class SlidingBuffer

Increments the slice number by one.

shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class VoxelsAssignerFactory

Shifts all coordinates backwards before passing to another VoxelsAssigner.

shiftBackBy(ReadableTuple3i) - Method in class ObjectMask

Shifts the object-mask by moving its bounding-box backwards.

shiftBackBy(ReadableTuple3i) - Method in class BoundingBox

Shifts the bounding-box backwards.

shiftBy(T, ReadableTuple3i) - Method in interface AccessObjectMask

Positionally-shifts an element by a given quantity in the positive direction.

shiftBy(ObjectMask, ReadableTuple3i) - Method in class AccessObjectMaskSimple

shiftBy(ReadableTuple3i) - Method in class ObjectCollection

Shifts the bounding-box of each object by adding to it.

shiftBy(ReadableTuple3i) - Method in class ObjectMask

Shifts the object-mask by moving its bounding-box forwards.

shiftBy(ReadableTuple3i) - Method in class BoundingBox

Shifts the bounding-box forwards.

shiftTo(Point3i) - Method in class BoundingBox

Assigns a new corner-location to the bounding-box.

shiftToOrigin() - Method in class ObjectMask

Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0).

shiftToOrigin() - Method in class BoundingBox

Moves the bounding-box to the origin (0,0,0) but preserves the extent.

shiftToZ(int) - Method in class BoundingBox

Assigns a new z-slice corner-location to the bounding-box.

SHORT_OPTION_DEBUG - Static variable in class CommandLineOptions

Enables debug-mode: runs only the first available input [whose name contains string].

SHORT_OPTION_HELP - Static variable in class CommandLineOptions

Displays help message with all command-line options.

SHORT_OPTION_INPUT - Static variable in class CommandLineOptions

Changes inputs.

SHORT_OPTION_INPUT_COPY_NON_INPUTS - Static variable in class CommandLineOptions

Additionally copies any files in the input directory, unused as inputs.

SHORT_OPTION_INPUT_RELATIVE - Static variable in class CommandLineOptions

Derives the unique identifier from the **entire relative filename or path** (excluding file extension).

SHORT_OPTION_INPUT_SHUFFLE - Static variable in class CommandLineOptions

Shuffles the order of the inputs.

SHORT_OPTION_INPUT_SUBSET_IDENTIFIER - Static variable in class CommandLineOptions

Subsets the identifier.

SHORT_OPTION_LOG_ERROR - Static variable in class CommandLineOptions

Logs initial BeanXML errors in greater detail to a file-path.

SHORT_OPTION_OUTPUT - Static variable in class CommandLineOptions

Changes output manager.

SHORT_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class CommandLineOptions

Output console only.

SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class CommandLineOptions

Disables specific output(s).

SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class CommandLineOptions

Enables all outputs.

SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class CommandLineOptions

Enables specific output(s).

SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT - Static variable in class CommandLineOptions

Suggests an output image file format: e.g -of jpg or -of ome.xml.

SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER - Static variable in class CommandLineOptions

Outputs with an incrementing number instead of the input identifier.

SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER - Static variable in class CommandLineOptions

Ignores the experiment identifier, when forming an output-path.

SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES - Static variable in class CommandLineOptions

Suppressed the subdirectory structure when outputting file identifiers.

SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class CommandLineOptions

Shows additional argument information, otherwise executes as normal.

SHORT_OPTION_SHOW_TASKS - Static variable in class CommandLineOptions

Prints the names of predefined tasks that can be easily used with -t.

SHORT_OPTION_TASK - Static variable in class CommandLineOptions

Changes task.

SHORT_OPTION_TASK_NUMBER_PROCESSORS - Static variable in class CommandLineOptions

Suggests a maximum number of processors to use for the task.

SHORT_OPTION_TASK_SIZE - Static variable in class CommandLineOptions

Suggests dimensions or a scaling factor for certain tasks.

SHORT_OPTION_VERSION - Static variable in class CommandLineOptions

Displays version and authorship information.

shouldOverwriteVoxelWithConstant(int, int) - Method in class ArithmeticWithConstantConditionallyWriteBase

Whether to overwrite the current voxel-value with the constant?

shouldOverwriteVoxelWithConstant(int, int) - Method in class MaxWithConstant

shouldOverwriteVoxelWithConstant(int, int) - Method in class MinWithConstant

shouldVisitPoint(Point3i, int) - Method in interface ConsiderVisit

Determines whether to visit a point or not.

Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme

Randomizes the order of colors in a list created by another ColorScheme.

Shuffle(ColorScheme) - Constructor for class Shuffle

Creates with a specific delegate ColorScheme.

Shuffle() - Constructor for class Shuffle

shuffle() - Method in class ColorList

Randomize the order of the colors in the list.

Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input

Randomly shuffles the order of the inputs.

Shuffle() - Constructor for class Shuffle

ShuffleIfRequested<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input

Shuffles inputs if it is requested in the InputContextParameters otherwise does not.

ShuffleIfRequested() - Constructor for class ShuffleIfRequested

SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype

A 16-bit voxel data-type representing signed-short numbers.

SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype

Base class for voxel-data-types that are signed and integral.

SignedVoxelType(int, String, long, long) - Constructor for class SignedVoxelType

Construct for a particular number of bits, with a unique identifier, and with bounds on the values.

SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io

Deletes any annotation when it is represented by a single file.

SimpleAnnotationDeleter() - Constructor for class SimpleAnnotationDeleter

SimpleManifestDeserializer - Class in org.anchoranalysis.io.manifest.deserializer

SimpleManifestDeserializer() - Constructor for class SimpleManifestDeserializer

SimpleName - Class in org.anchoranalysis.feature.io.name

A name with only one part, and is always unique.

SimpleName(String) - Constructor for class SimpleName

SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name

A simple container expressing a name-value pair.

SimpleNameValue(String, V) - Constructor for class SimpleNameValue

SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle

SimpleOutputNameStyle(String) - Constructor for class SimpleOutputNameStyle

SimpleOverlayWriter - Class in org.anchoranalysis.mpp.io.marks.generator

Converts a configuration to a set of object-masks, using a simple DrawObject for all objects.

SimpleOverlayWriter(DrawObject) - Constructor for class SimpleOverlayWriter

SimulatedAnnealing<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme

Finds an optima using a simulated-annealing approach

SimulatedAnnealing() - Constructor for class SimulatedAnnealing

Single - Class in org.anchoranalysis.image.bean.spatial.arrange

Single() - Constructor for class Single

Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition

Single() - Constructor for class Single

SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score

A score that is calculated on a single channel only

SingleChannel() - Constructor for class SingleChannel

SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map

For an image with a single channel

SingleChannel() - Constructor for class SingleChannel

SingleChannel(String) - Constructor for class SingleChannel

singleChannelMaybe3D(boolean) - Static method in class StackWriteAttributesFactory

SingleColor - Class in org.anchoranalysis.core.color

An index that always uses the same single color

SingleColor(Color) - Constructor for class SingleColor

Creates with a particular color.

SingleColor(RGBColor) - Constructor for class SingleColor

SingleFile - Class in org.anchoranalysis.io.input.bean.files

SingleFile(String) - Constructor for class SingleFile

SingleFile() - Constructor for class SingleFile

SingleFileInputBase - Class in org.anchoranalysis.io.input.file

A base class for inputs that refer to a single file.

SingleFileInputBase(NamedFile) - Constructor for class SingleFileInputBase

SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator

A Generator that eventually writes only a single file to the filesystem.

SingleFileTypeGenerator() - Constructor for class SingleFileTypeGenerator

SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator

Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.

SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class SingleFileTypeGeneratorBridge

SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single

Outputs are enabled if they are contained in both of two SingleLevelOutputEnabled.

SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelAnd

Creates using two SingleLevelOutputEnableds.

SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single

Base class for a SingleLevelOutputEnabled that combines two existing such classes.

SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelBinary

SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single

Outputs are enabled if they are contained in a set.

SingleLevelInSet(Set<String>) - Constructor for class SingleLevelInSet

SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single

The complement of an existing SingleLevelOutputEnabled where disabled outputs are enabled, and vice-versa.

SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class SingleLevelNot

SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single

Outputs are enabled if they are contained in either of two SingleLevelOutputEnabled.

SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelOr

Creates using two SingleLevelOutputEnableds.

SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single

SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider

Provides (maybe) a single mark

SingleMarkProvider() - Constructor for class SingleMarkProvider

SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy

A base class for implementations of AnnotatorStrategy where a single unique path exists for every annotation.

SinglePathStrategy() - Constructor for class SinglePathStrategy

SingleRowPerInput<T extends InputFromManager,S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source

Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.

SingleRowPerInput(String) - Constructor for class SingleRowPerInput

Creates with a single non-group header that should be describe an identifier.

SingleRowPerInput(String[]) - Constructor for class SingleRowPerInput

SingleTableCalculator - Class in org.anchoranalysis.image.feature.calculator

SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class SingleTableCalculator

size() - Method in class ColorList

The number of elements (colors) in the list.

size() - Method in class NameValueMap

The number of elements in the set.

size() - Method in class FeatureList

Returns the number of elements in this list.

size() - Method in class LabelledResultsVector

The number of calculations stored in the vector.

size() - Method in class FeatureNameList

The number of names in the list.

size() - Method in class ResultsVector

The number of calculations stored in the vector.

size() - Method in class ResultsVectorList

The number of ResultsVectors in the list.

size() - Method in class NamedFeatureStore

The total number of Features in the store.

size() - Method in class ObjectCollectionWithProperties

Number of elements in the collection.

size() - Method in class ScaledElements

Number of scaled-elements.

size() - Method in class NamedStacks

Number of stacks.

size() - Method in class StackSeries

size() - Method in class TimeSequence

size() - Method in class IntersectingObjects

Number of items in the r-tree.

size() - Method in class ObjectCollection

The number of objects in the collection.

size() - Method in interface VoxelStatistics

The total count.

size() - Method in class VoxelStatisticsCombined

size() - Method in class VoxelStatisticsFromHistogram

size() - Method in class Histogram

The size of the range of values in the histogram.

size() - Method in class BoundUnitless

size() - Method in class MarksWithEnergyBreakdown

size() - Method in class MarksWithTotalEnergy

size() - Method in class VoxelizedMarksWithEnergy

size() - Method in class EnergySavedInd

size() - Method in class EnergyMemoList

size() - Method in class MemoList

size() - Method in class UpdatableMarksList

size() - Method in class IndexByChannel

size() - Method in class ColoredMarks

size() - Method in class MarkCollection

size() - Method in interface MemoForIndex

size() - Method in class TerminationConditionListOr

size() - Method in class WeightedKernelList

size() - Method in class ColoredOverlayCollection

size() - Method in class OverlayCollection

size() - Method in class ListWithThumbnails

size() - Method in class ParsedFilePathBag

size() - Method in class ContiguousVoxelPath

size() - Method in class LoopablePoints

Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind

Size() - Constructor for class Size

size() - Method in class BoundedList

The number of elements.

size() - Method in class RTree

The total number of items stored in the tree.

sizeC(IFormatReader) - Method in class Default

sizeC(IFormatReader) - Method in class ForceNumberChannels

sizeC(IFormatReader) - Method in class ReadOptions

Number of channels.

sizeC(IFormatReader) - Method in class ReadOptionsDelegate

sizeCurrentLoad() - Method in class LRUCache

Number of items currently in the cache.

sizeDescriptor(Extent) - Method in class HOGParameters

Calculates the size of the descriptor will be for a given image.

SizeExtents - Class in org.anchoranalysis.plugin.io.multifile

Remembers the different sizes among the files

SizeExtents(ParsedFilePathBag) - Constructor for class SizeExtents

sizeFeatures() - Method in interface FeatureCalculatorMulti

The number of features that is calculated on each call to FeatureCalculatorMulti.calculate(T), and therefore the size of the returned ResultsVector.

sizeFeatures() - Method in class FeatureCalculatorMultiChangeInput

sizeFeatures() - Method in class SequentialSession

sizeFeatures() - Method in class PairsTableCalculator

sizeFeatures() - Method in class SingleTableCalculator

sizeFirst() - Method in class CostMatrix

The number of elements in the first list.

sizeSecond() - Method in class CostMatrix

The number of elements in the second list.

sizeT(Progress, Logger) - Method in interface NamedChannelsForSeries

sizeT(Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate

sizeT(Progress, Logger) - Method in class NamedChannelsForSeriesMap

sizeT(IFormatReader) - Method in class Default

sizeT(IFormatReader) - Method in class ForceNumberFrames

sizeT(IFormatReader) - Method in class ForceTimeSeriesToStack

sizeT(IFormatReader) - Method in class ReadOptions

Number of time-points (frames in a time series).

sizeT(IFormatReader) - Method in class ReadOptionsDelegate

SizeXY - Class in org.anchoranalysis.image.bean.spatial

SizeXY(Extent) - Constructor for class SizeXY

Constructor

SizeXY() - Constructor for class SizeXY

SizeXY(int, int) - Constructor for class SizeXY

sizeZ(IFormatReader) - Method in class Default

sizeZ(IFormatReader) - Method in class ForceTimeSeriesToStack

sizeZ(IFormatReader) - Method in class ReadOptions

Number of z-slices (slices in a 3D image).

sizeZ(IFormatReader) - Method in class ReadOptionsDelegate

skewness(Histogram) - Static method in class HistogramStatistics

Calculates the skewness of a distribution of values, represented by their histogram.

Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

Calculates the skewness of all the values in the histogram.

Skewness() - Constructor for class Skewness

SkipInit - Annotation Type in org.anchoranalysis.bean.annotation

Indicates that this particular bean-field should be ignored during (recursive) initialization.

slice(int) - Method in class BinaryVoxels

A VoxelBuffer corresponding to a particular z-slice.

slice(int) - Method in class FromByte

slice(int) - Method in class FromFloat

slice(int) - Method in class FromInt

slice(int) - Method in class FromShort

slice(int) - Method in interface SliceBufferIndex

A VoxelBuffer corresponding to a particular z-slice.

slice(int) - Method in interface VoxelsExtracter

Creates a new Voxels with only particular slice.

slice(int) - Method in class Voxels

A VoxelBuffer corresponding to a particular z-slice.

slice(int) - Method in class VoxelsUntyped

A VoxelBuffer corresponding to a particular z-slice.

SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice

SliceAt() - Constructor for class SliceAt

sliceBinary(int) - Method in class BinaryVoxels

A particular z-slice, wrapped into a BinaryVoxels.

sliceBuffer(int) - Method in class Mask

A buffer corresponding to a particular z-slice.

sliceBuffer(int, int) - Method in class RGBStack

A buffer corresponding to a particular z-slice of a particular channel.

sliceBuffer(int) - Method in class BinaryVoxels

A buffer corresponding to a particular z-slice.

sliceBuffer(int) - Method in interface SliceBufferIndex

The underlying buffer corresponding to a particular z-slice.

sliceBuffer(int) - Method in class Voxels

A buffer corresponding to a particular z-slice.

sliceBufferGlobal(int) - Method in class BoundedVoxels

A slice buffer with global coordinates.

sliceBufferGlobal(int) - Method in class ObjectMask

A slice buffer with global coordinates.

SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.buffer.slice

A container with voxel-buffers for each z-slice.

sliceBufferLocal(int) - Method in class ObjectWithProperties

A slice buffer with local coordinates.

sliceBufferLocal(int) - Method in class BoundedVoxels

A slice buffer with local coordinates.

sliceBufferLocal(int) - Method in class ObjectMask

A slice buffer with local coordinates.

slices() - Method in class BinaryVoxels

An index mapping slice of voxels (in the z dimension) to a particular buffer with the corresponding voxel intensities.

slices() - Method in class Voxels

An index mapping slice of voxels (in the z dimension) to a particular buffer with the corresponding voxel intensities.

sliceStatisticsForRegion(VoxelizedMark, int) - Method in class IndexedRegionBase

SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice

Segmenting a z-Stack slice-by-slice.

SliceThresholder(BinaryValuesByte) - Constructor for class SliceThresholder

SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice

SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class SliceThresholderMask

SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice

SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class SliceThresholderWithoutMask

SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer

An index that places a particular z-slice in local context.

SlidingBuffer(Voxels<T>) - Constructor for class SlidingBuffer

Create for particular voxels.

Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient

3x3 Sobel Filter

Sobel() - Constructor for class Sobel

solveQuadraticEquation(double, double, double) - Static method in class QuadraticEquationSolver

Solves a quadratic equation in form x^2 + b^x + c = 0.

sort(Comparator<Feature<T>>) - Method in class FeatureList

Creates a new feature-list sorted in a particular order.

SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.file.provider

SortAlphabetically() - Constructor for class SortAlphabetically

SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input

Sorts the input-items in alphabetical order of their input-name.

SortAlphabetically() - Constructor for class SortAlphabetically

SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider

SortAlphabeticallyWithDirectory() - Constructor for class SortAlphabeticallyWithDirectory

SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature

Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)

SortByFeature() - Constructor for class SortByFeature

SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile

SortedSetChannel() - Constructor for class SortedSetChannel

SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile

SortedSetSlice(String, int) - Constructor for class SortedSetSlice

sourceIncrement - Variable in class ConvertTo

The number of elements (bytes) to increment by, when iterating through the source buffer.

sourceSize - Variable in class ConvertTo

The total number of elements (always bytes) in the source buffer.

sourceValue - Variable in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer

The intensity value of the source voxel.

spatiallySeparate() - Method in class IntersectingObjects

Splits the collection of objects into spatially separate clusters.

SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree

Splits a collection of elements into spatially separate clusters.

SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class SpatiallySeparate

SpatialUnits - Class in org.anchoranalysis.image.core.dimensions

Units to describe spatial quantities.

SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions

Suffix that describes a particular quantity of units (micron, nano, square microns etc.)

Specific - Class in org.anchoranalysis.plugin.mpp.bean.region

Specific() - Constructor for class Specific

SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels

Selects a specific set of channels from stacks, each identified by a stack-name and channel index

SpecificAndRename() - Constructor for class SpecificAndRename

SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments

A feature based one one-specific principal-axis as identified by image moments.

SpecificAxisBase() - Constructor for class SpecificAxisBase

SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled

Only specific outputs, identified by a textual name, are disabled, and all others are enabled.

SpecificDisabled() - Constructor for class SpecificDisabled

SpecificDisabled(StringSet) - Constructor for class SpecificDisabled

SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled

Only specific outputs, identified by a textual name, are enabled.

SpecificEnabled() - Constructor for class SpecificEnabled

SpecificEnabled(StringSet) - Constructor for class SpecificEnabled

SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy

SpecificEnergyChannelBase() - Constructor for class SpecificEnergyChannelBase

SpecificPathList - Class in org.anchoranalysis.io.input.bean.files

A specific list of paths which form the input.

SpecificPathList(List<String>) - Constructor for class SpecificPathList

SpecificPathList(StringList) - Constructor for class SpecificPathList

SpecificPathList() - Constructor for class SpecificPathList

SpecifyDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider

Specifies dimensions explicitly via bean properties.

SpecifyDimensions(int, int) - Constructor for class SpecifyDimensions

Create with specific lengths for X and Y dimensions.

SpecifyDimensions(SizeXY) - Constructor for class SpecifyDimensions

Create with specific lengths for X and Y dimensions.

SpecifyDimensions() - Constructor for class SpecifyDimensions

Sphere - Class in org.anchoranalysis.mpp.mark.conic

A sphere

Sphere(Bound) - Constructor for class Sphere

Creates with a radius within particular bounds.

Sphere(Sphere) - Constructor for class Sphere

Copy Constructor

Sphere() - Constructor for class Sphere

split(Path) - Method in class RootPath

It splits the root portion of a path from the remainder.

split(Path, String, boolean) - Method in class RootPathMap

Given a path, it splits the *root* portion of the path from the remainder, trying a root identified by the rootName and debugMode (and if this fails, also trying with debugMode==false)

SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split

SplitByObjects() - Constructor for class SplitByObjects

SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean

Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.

SplitContourAtSaddlePoints() - Constructor for class SplitContourAtSaddlePoints

splitFilename(String) - Static method in class ExtensionUtilities

Splits the file-name of a path into a base part and an extension part.

SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split

Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).

SplitIntoSquares() - Constructor for class SplitIntoSquares

SplitPath - Class in org.anchoranalysis.core.system.path

A path that has been split into two components: a root and a remainder.

SplitPath(Path, Path) - Constructor for class SplitPath

Stack - Class in org.anchoranalysis.image.core.stack

One or more single-channel images that all have the same dimensions.

Stack() - Constructor for class Stack

Creates a new empty Stack that will not become an RGB image after adding channels.

Stack(boolean) - Constructor for class Stack

Creates a new empty Stack and whether it will become an RGB image or not.

Stack(Channel) - Constructor for class Stack

Creates a Stack with a single channel.

Stack(Extent) - Constructor for class Stack

Creates a Stack with a single unsigned-byte channel of size channel.

Stack(Dimensions, ChannelFactorySingleType, int, boolean) - Constructor for class Stack

Create with a particular number of empty Channels.

Stack(boolean, Channel...) - Constructor for class Stack

Creates from a varying number of channels, and a flag to indicate if they represent an RGB image or not.

Stack(Stream<Channel>) - Constructor for class Stack

Create a Stack from a stream of Channels.

Stack(boolean, Stream<Channel>) - Constructor for class Stack

Like Stack(Stream) but allows explicitly setting whether it should be interpreted as RGB or not.

stack() - Method in class MultiInput

stack(String) - Static method in class ReferenceFactory

StackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator

Writes a stack to the filesystem.

StackGenerator(String, boolean) - Constructor for class StackGenerator

Creates a generator that performs no padding.

StackGenerator(boolean, Optional<String>, boolean) - Constructor for class StackGenerator

Creates the generator from a stack, inferring whether all stacks will be 2D from this stack's dimensions.

StackGenerator(boolean, Optional<String>, StackWriteAttributes) - Constructor for class StackGenerator

StackIdentifiers - Class in org.anchoranalysis.image.io.stack

Common identifiers used for storing particular types of images.

StackNotUniformSized - Class in org.anchoranalysis.image.core.stack

A list of Channels that are permitted to vary in size.

StackNotUniformSized() - Constructor for class StackNotUniformSized

Creates an empty with no channels.

StackNotUniformSized(Stream<Channel>) - Constructor for class StackNotUniformSized

Creates from a stream of Channels.

StackNotUniformSized(Channel) - Constructor for class StackNotUniformSized

Creates from a single Channel.

StackProvider - Class in org.anchoranalysis.image.bean.provider.stack

Base class for beans that implement Provider to provide a Stack.

StackProvider() - Constructor for class StackProvider

StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack

StackProviderUnary() - Constructor for class StackProviderUnary

StackProviderWithLabel - Class in org.anchoranalysis.image.io.bean.stack.combine

StackProviderWithLabel(Stack, String) - Constructor for class StackProviderWithLabel

StackProviderWithLabel() - Constructor for class StackProviderWithLabel

StackReader - Class in org.anchoranalysis.image.io.bean.stack.reader

Reads an image-Stack from the file-system.

StackReader() - Constructor for class StackReader

StackReaderOrientationCorrection - Class in org.anchoranalysis.image.io.bean.stack.reader

A StackReader that supports the correction of orientation as images are read from the file-system.

StackReaderOrientationCorrection() - Constructor for class StackReaderOrientationCorrection

StackRGBState - Enum in org.anchoranalysis.image.io.stack.output

Whether a stack is RGB or RGBA or neither.

stacks(Logger) - Method in class AnnotationWithStrategy

All stacks associated with the input, lazily evaluated.

stacks() - Method in class ImageInitialization

STACKS - Static variable in class OutputterDirectories

Where stacks are typically placed in a define-experiment output

Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack

An InputManager where each file provides one or more Stacks.

Stacks(InputManager<FileInput>) - Constructor for class Stacks

Stacks() - Constructor for class Stacks

StackSequenceInput - Interface in org.anchoranalysis.image.io.stack.input

Provides a single stack (or a time series of such stacks) as an input

StackSeries - Class in org.anchoranalysis.image.io.stack

StackSeries() - Constructor for class StackSeries

stackTrace() - Method in exception AnchorFriendlyCheckedException

Prints a stack trace of the current exception to a string.

StackWithMap - Class in org.anchoranalysis.mpp.io.input

Combines a Stack with a map of other stacks

StackWithMap(String, ProvidesStackInput) - Constructor for class StackWithMap

StackWriteAttributes - Class in org.anchoranalysis.image.io.stack.output

Attributes describing stack which may determine which writer is used.

StackWriteAttributes(boolean, boolean, boolean, StackRGBState, boolean) - Constructor for class StackWriteAttributes

Alternative constructor that assumes each channel is 8-bits.

StackWriteAttributesFactory - Class in org.anchoranalysis.image.io.stack.output

Creates StackWriteAttributes to describe certain attributes.

StackWriteOptions - Class in org.anchoranalysis.image.io.stack.output

A combination of attributions describing how to write a particular stack and any suggestions from the user.

StackWriteOptions(StackWriteAttributes, Optional<ImageFileFormat>) - Constructor for class StackWriteOptions

StackWriter - Class in org.anchoranalysis.image.io.bean.stack.writer

Writes a stack (i.e.

StackWriter() - Constructor for class StackWriter

StackWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer

A base class for a StackWriter delegates to another StackWriter based on values of a StackWriteAttributes.

StackWriterDelegateBase() - Constructor for class StackWriterDelegateBase

StandardDeviation - Class in org.anchoranalysis.feature.bean.results

The standard-deviation of the results from a particular feature.

StandardDeviation() - Constructor for class StandardDeviation

standardDeviation() - Method in class Histogram

Calculates the standard-deviation of the distribution represented by the histogram.

start() - Method in class StatefulNullMessageLogger

start() - Method in class ConsoleMessageLogger

start() - Method in class FailureOnlyMessageLogger

start() - Method in class MessageLoggerList

start() - Method in interface StatefulMessageLogger

start() - Method in class TextFileMessageLogger

start(FeatureInitialization, SharedFeatures, Logger) - Method in class SequentialSession

Starts the session

start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in interface FeatureTableCalculator

Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object

start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class PairsTableCalculator

start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class SingleTableCalculator

start() - Method in class TextFileOutput

start(EnergyStack) - Method in class CheckMark

Called before any calls to CheckMark.check(org.anchoranalysis.mpp.mark.Mark, org.anchoranalysis.mpp.bean.regionmap.RegionMap, org.anchoranalysis.feature.energy.EnergyStack)

start(FeedbackBeginParameters<T>) - Method in class AggregateTriggerBank

start(Optional<Dimensions>, ObjectCollection) - Method in class DiscardOutliers

start(Optional<Dimensions>, ObjectCollection) - Method in class RelationWithMatches

start(Optional<Dimensions>, ObjectCollection) - Method in class GreaterIntersectionWith

start(Optional<Dimensions>, ObjectCollection) - Method in class IntensityGreaterEqualThan

start(Optional<Dimensions>, ObjectCollection) - Method in class IntersectsWith

start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedFeature

start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedVolume

start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterPredicate

start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterRelation

start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class OutlinePreserveRelativeSize

start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class ThumbnailFromObjects

Initializes a batch to create thumbnails.

start() - Method in class ScaleToSize

start() - Method in class ThumbnailFromStack

Should always be called once before any calls to ThumbnailFromStack.thumbnailFor(org.anchoranalysis.image.core.stack.Stack)

start(EnergyStack) - Method in class AndList

start(EnergyStack) - Method in class FeatureValueCheckMark

startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class CombineObjectsForFeatures

Derives a list of inputs from an object-collection

startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class EachObjectIndependently

startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class PairNeighbors

startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class ConvertImageFormat

startSeries(S, U, InputOutputContext) - Method in class RasterTask

Starts processing of a series.

startSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class MovieFromSlices

StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log

A MessageLogger that can be started and stopped, and is aware this state.

StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log

Does nothing (i.e.

StatefulNullMessageLogger() - Constructor for class StatefulNullMessageLogger

StateReporter<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback

Converts the optimization state to a form that the reporter needs

StateReporter() - Constructor for class StateReporter

stateReporter() - Method in class AssignMode

stateReporter() - Method in class DirectAssignMode

stateReporter() - Method in class TransformationAssignMode

StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter

Assumes the state is reported without any transformation

StateReporterIdentity() - Constructor for class StateReporterIdentity

StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter

Assumes we are interested in VoxelizedMarksWithEnergy as reporting type, and our optimization-state is in the form ToPixelized<T>

StateReporterToPixelized() - Constructor for class StateReporterToPixelized

StateReporterTransformer<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter

StateReporterTransformer() - Constructor for class StateReporterTransformer

stateToKernel() - Method in class KernelStateBridge

stateToKernel() - Method in class KernelStateBridgeIdentity

stateToKernel() - Method in class KernelStateBridgePixelize

stateToKernel() - Method in class KernelStateBridgeTransformer

StateTransformer<W,X> - Interface in org.anchoranalysis.mpp.segment.transformer

StateTransformerBean<S,T> - Class in org.anchoranalysis.mpp.segment.transformer

Transforms one type into another

StateTransformerBean() - Constructor for class StateTransformerBean

StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path

StaticFilePath() - Constructor for class StaticFilePath

StatisticalBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics

Calculates a score based upon the statistical mean and std-deviation.

StatisticalBase() - Constructor for class StatisticalBase

statisticFromFeatureValue(DoubleArrayList) - Method in class FeatureResultsStatistic

Calculates the statistic for a given list of result-value.

statisticFromFeatureValue(DoubleArrayList) - Method in class Mean

statisticFromFeatureValue(DoubleArrayList) - Method in class Quantile

statisticFromFeatureValue(DoubleArrayList) - Method in class StandardDeviation

statisticFromFeatureValue(DoubleArrayList) - Method in class Sum

statistics() - Method in interface Assignment

The statistics associated with the assignment.

statistics() - Method in class ObjectVoxelIntersection

statistics() - Method in class OverlappingObjects

statisticsFor(int, int, int) - Method in interface VoxelizedMark

statisticsForAllGroups() - Method in class ComparisonSharedState

statisticsForAllSlices(int, int) - Method in interface VoxelizedMark

statisticsForAllSlices(VoxelizedMark, boolean) - Method in class SelectSlicesWithIndexBase

statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface VoxelizedMark

StatisticsToExport - Class in org.anchoranalysis.annotation.io.comparer

Statistics to be exported, comprised of name-value pairs.

StatisticsToExport() - Constructor for class StatisticsToExport

stdDev() - Method in interface VoxelStatistics

The standard-deviation of all voxel values.

StdDev - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

StdDev() - Constructor for class StdDev

Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding

Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class Steepest

Create for a specific buffer.

steepestDescent(Point3i, int, int) - Method in class Steepest

StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store

Supplier of an object for a store.

stream() - Method in class DoubleSet

Creates a stream of elements in the set.

stream() - Method in class IntegerSet

Creates a stream of elements in the set.

stream() - Method in class StringSet

Creates a stream of elements in the set.

stream() - Method in class StreamableCollection

A single instance of the stream from the supplier.

stream() - Method in class NameValueMap

Exposes the elements in the set as a stream.

stream() - Method in class ResultsVectorList

A stream of ResultsVectors.

stream() - Method in class ObjectCollection

Provides various functional-programming operations on the object-collection.

stream() - Method in class ImageCounterList

stream() - Method in class BoundedList

A stream of elements in the list.

StreamableCollection<T> - Class in org.anchoranalysis.core.functional

As a stream can only be used once, this data-structure allows for repeatedly getting streams from a collection.

StreamableCollection(Collection<T>) - Constructor for class StreamableCollection

Create for a particular collection

StreamableCollection(Supplier<Stream<T>>) - Constructor for class StreamableCollection

streamIndices(Collection<Integer>) - Method in class ObjectCollection

Streams only objects at specific indices.

streamOverZ() - Method in class Extent

Streams over the range of z values.

streamStandardJava() - Method in class ObjectCollection

A stream of object-masks as per Java's standard collections interface.

StringGenerator - Class in org.anchoranalysis.io.generator.text

StringGenerator() - Constructor for class StringGenerator

StringList - Class in org.anchoranalysis.bean.primitive

A bean defining a list of Strings.

StringList() - Constructor for class StringList

Constructs with an empty list.

StringList(String...) - Constructor for class StringList

Constructs, populated with one or more values.

StringList(List<String>) - Constructor for class StringList

Constructs, populated with a list of strings.

StringListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive

Creates a StringList from a XML element.

StringListFactory() - Constructor for class StringListFactory

StringMap - Class in org.anchoranalysis.bean.shared

A bean that defines a mapping between a set of Strings to another set of Strings.

StringMap() - Constructor for class StringMap

StringMapItem - Class in org.anchoranalysis.bean.shared

A bean with a pair of strings, representing a mapping from one string to the other.

StringMapItem() - Constructor for class StringMapItem

stringRepresentationForElement(int) - Method in interface IncompleteElementRange

Returns the typed-index corresponding to the integer-index.

StringSet - Class in org.anchoranalysis.bean.primitive

A bean defining a set of Strings.

StringSet(String...) - Constructor for class StringSet

Constructs with one or more values added to the list.

StringSet() - Constructor for class StringSet

StringSet(Set<String>) - Constructor for class StringSet

StringSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive

Creates a StringSet from a XML element.

StringSetFactory() - Constructor for class StringSetFactory

StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle

StringSuffixOutputNameStyle() - Constructor for class StringSuffixOutputNameStyle

StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class StringSuffixOutputNameStyle

StringsWithoutOrder - Class in org.anchoranalysis.io.manifest.sequencetype

A sequence of strings that has no order.

StringsWithoutOrder() - Constructor for class StringsWithoutOrder

StringUtilities - Class in org.anchoranalysis.core.value

Utility functions for manipualting strings.

strMarks() - Method in class MarkWithPositionAndSingleRadius

strPos() - Method in class MarkWithPosition

subdirectories() - Method in class MutableDirectory

The MutableDirectory in the manifest for any subdirectories.

Subdirectory - Class in org.anchoranalysis.io.manifest.directory

A SubdirectoryBase entry in the manifest for a subdirectory.

Subdirectory(Path) - Constructor for class Subdirectory

Subdirectory() - Constructor for class Subdirectory

subdirectory(String, ManifestDirectoryDescription, boolean) - Method in interface InputOutputContext

Creates a new context that writes instead to a subdirectory.

SubdirectoryBase - Class in org.anchoranalysis.io.manifest.directory

SubdirectoryBase(Path) - Constructor for class SubdirectoryBase

SubdirectoryBase() - Constructor for class SubdirectoryBase

subdirectoryForGroupOutputs() - Method in class GroupedStackBase

An optional subdirectory where the group outputs are placed.

subdirectoryForGroupOutputs() - Method in class ExportImageHistograms

subdirectoryForGroupOutputs() - Method in class GroupedMeanChannelTask

subList(int, int) - Method in class UpdatableMarksList

SUBMARK_CORE - Static variable in class GlobalRegionIdentifiers

SUBMARK_CORE_INNER - Static variable in class GlobalRegionIdentifiers

SUBMARK_INSIDE - Static variable in class GlobalRegionIdentifiers

SUBMARK_OUTSIDE - Static variable in class GlobalRegionIdentifiers

SUBMARK_SHELL - Static variable in class GlobalRegionIdentifiers

SUBMARK_SHELL_OUTSIDE - Static variable in class GlobalRegionIdentifiers

SubmittedJob - Class in org.anchoranalysis.experiment.task.processor

SubmittedJob(JobDescription, JobState) - Constructor for class SubmittedJob

subset(StringSet) - Method in class NamedStacks

Creates a new collection containing only items whose keys exist in a particular set.

subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class SharedFeatures

Extracts the subset of inputs that are compatible with a particular input-type.

SubsetRangeIfRequested - Class in org.anchoranalysis.plugin.io.bean.file.namer

If specified in the context, the existing name if subsetted according to an index range.

SubsetRangeIfRequested() - Constructor for class SubsetRangeIfRequested

subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class ColoredMarks

subsetWhereBBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class ColoredOverlayCollection

SubstituteRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming

A regular expression substitution (replaceAll) is applied to the relative-path

SubstituteRegularExpression() - Constructor for class SubstituteRegularExpression

subtract(VarianceCalculatorDouble) - Method in class VarianceCalculatorDouble

Subtracts the running-sums and count from another VarianceCalculatorDouble from the current object's state.

subtract(VarianceCalculatorLong) - Method in class VarianceCalculatorLong

Subtracts the running-sums and count from another VarianceCalculatorLong from the current object's state.

subtract(Tuple3d) - Method in class Tuple3d

Arithmetically subtract a Tuple3d's values across each dimension.

subtract(int) - Method in class Tuple3i

Arithmetically subtracts a value across each dimension.

subtract(ReadableTuple3i) - Method in class Tuple3i

Arithmetically subtracts a value across each dimension.

subtractFrom(int) - Method in interface VoxelsArithmetic

Subtracts all current voxel-values from a constant-value.

SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic

SubtractFrom() - Constructor for class SubtractFrom

SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

SubtractFromConstant() - Constructor for class SubtractFromConstant

subtractFromMaxValue() - Method in class VoxelsUntyped

Subtracts all voxel-values from the maximum value associated with the data-type.

SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

Subtract the mean (of the entire channel or a masked portion thereof) from every voxel

SubtractMean() - Constructor for class SubtractMean

SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair

Calculates merged - reduce(first,second) for a FeatureInputPairObjects

SubtractReducedFromMerged() - Constructor for class SubtractReducedFromMerged

SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair

Subtract second-object from first-object in a pair.

SubtractSecondFromFirst() - Constructor for class SubtractSecondFromFirst

SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

SubtractTwoChannels(IntBinaryOperation) - Constructor for class SubtractTwoChannels

suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class SpatialUnits

A string that describes the suffix for meters.

SuggestionFormatException - Exception in org.anchoranalysis.image.core.dimensions.size.suggestion

An exception thrown by ImageSizeSuggestionFactory to indicate a format is invalid or unknown.

SuggestionFormatException(String) - Constructor for exception SuggestionFormatException

Create with a message only.

Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator

Sums the results after calculating a list of Features.

Sum(FeatureList<T>) - Constructor for class Sum

Create with a list of Features which become summed.

Sum() - Constructor for class Sum

Sum - Class in org.anchoranalysis.feature.bean.results

The sum of the results from a particular feature.

Sum() - Constructor for class Sum

sum() - Method in interface VoxelStatistics

The sum of all voxel values.

sum() - Method in class VoxelStatisticsCombined

sum() - Method in class VoxelStatisticsFromHistogram

sum() - Method in class AggIDCounter

Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

Sum() - Constructor for class Sum

sumExecutionTimeSeconds() - Method in class RecordedExecutionTimes.RecordedOperation

The total summed execution time in seconds for the operation.

summarize() - Method in exception BeanMisconfiguredXMLException

This summarize() option just looks for the most deep exception that can be 'combined' and takes its message

summarize() - Method in exception LocalisedBeanException

summarize() - Method in exception AnchorCombinableException

Creates a new {link Throwable} that summarizes this exception and any nested causes of the exception.

summarize() - Method in exception NamedProviderGetException

SummarizeBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task

SummarizeBase() - Constructor for class SummarizeBase

summarizeDisabled() - Method in class RecordedOutputs

A comma-separated string of all output-names that were not enabled.

summarizeEnabled() - Method in class RecordedOutputs

A comma-separated string of all output-names that were enabled.

summarizeIgnoreIdenticalFilePath(Path) - Method in exception LocalisedBeanException

If there is no nested-set of combinable exceptions, and the message related to this current exception is identical as the passed parameter, then we simply ignore the current exception and promote its Throwable.getCause().

SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task

SummarizeInputs() - Constructor for class SummarizeInputs

summarizeMultiplex(boolean) - Method in class RecordedOutputs

Multiplex between RecordedOutputs.summarizeEnabled() and RecordedOutputs.summarizeDisabled().

Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer

Summarizes a set of elements by outputting a descriptive string.

Summarizer() - Constructor for class Summarizer

SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer

Collects summary data about a set of input files that will eventually be outputted to the user

SummarizerAggregate() - Constructor for class SummarizerAggregate

SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer

A count of the number of inputs.

SummarizerCount() - Constructor for class SummarizerCount

SummarizerImageMetadata<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image

Summarizes ImageMetadataInput in different ways.

SummarizerImageMetadata() - Constructor for class SummarizerImageMetadata

SummarizerImageMetadataSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image

A simple summarizer, where there's one summary-item per image.

SummarizerImageMetadataSimple() - Constructor for class SummarizerImageMetadataSimple

SummarizerInputFromManager<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input

Extracts a particular item from an InputFromManager for further summarization downstream.

SummarizerInputFromManager() - Constructor for class SummarizerInputFromManager

SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer

Creates a string where each line is an element.

SummarizerListMultiline() - Constructor for class SummarizerListMultiline

SummarizerPath - Class in org.anchoranalysis.plugin.io.bean.summarizer.path

Base class for Summarizers that operate on the Path associated with inputs.

SummarizerPath() - Constructor for class SummarizerPath

SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer

Multiplexes between two summarizers depending on the total number of count.

SummarizerSplitMoreThan() - Constructor for class SummarizerSplitMoreThan

SummaryException - Exception in org.anchoranalysis.core.exception.combinable

A special kind of exception that represents a summary of an existing set of exceptions.

SummaryException(String, Throwable) - Constructor for exception SummaryException

Creates with a message and a cause.

sumOfSquares() - Method in interface VoxelStatistics

The sum of the square of all voxel values.

sumOfSquares() - Method in class VoxelStatisticsCombined

sumOfSquares() - Method in class VoxelStatisticsFromHistogram

sumOverlapFromPaired() - Method in class OverlappingObjects

Sums the overlap-ratio across all assigned pairs.

SupplierAtIndex<T> - Interface in org.anchoranalysis.io.manifest.directory.sequenced

supportsMultipleChannelsPerSourceBuffer() - Method in class ConvertTo

Whether the source buffer can encode more than one channel?

supportsMultipleChannelsPerSourceBuffer() - Method in class ToUnsignedByteWithScaling

supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedByteFromFloat

supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedByteFromUnsignedByte

supportsMultipleChannelsPerSourceBuffer() - Method in class ToFloat

supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedIntFromUnsignedInt

supportsMultipleChannelsPerSourceBuffer() - Method in class ToUnsignedShort

SupportsTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer

Base class for ImageJRasterWriter that does support writing time-series as a stack.

SupportsTimeSeries() - Constructor for class SupportsTimeSeries

suppressedLogger() - Static method in class LoggingFixture

A Logger that doesn't output anything.

suppressedMessageLogger() - Static method in class LoggingFixture

A MessageLogger that doesn't output anything.

SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface

The number of voxel-faces along the surface (the faces of each voxel that touch outside)

SurfaceNumberVoxelFaces() - Constructor for class SurfaceNumberVoxelFaces

SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface

The number of voxels on the surface (all voxels on the exterior of the object)

SurfaceNumberVoxels() - Constructor for class SurfaceNumberVoxels

SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface

SurfaceNumberVoxelsBase() - Constructor for class SurfaceNumberVoxelsBase

SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind

SurfaceSizeMaskNonZero() - Constructor for class SurfaceSizeMaskNonZero

SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options

Treats the channel index as if it's time, and vice versa

SwitchChannelTime() - Constructor for class SwitchChannelTime

SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log

Switches between two log-reporters depending on whether detailed logging is switched on or not

SwitchDetailedLogging() - Constructor for class SwitchDetailedLogging

T

TableItemArrangement<T> - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange

TableItemArrangement(TableItemArrangement.TableCreator<T>, int, int) - Constructor for class TableItemArrangement

TableItemArrangement.TableCreator<T> - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange

TableItemException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange

TableItemException(String) - Constructor for exception TableItemException

TableItemException(Exception) - Constructor for exception TableItemException

tail() - Method in class ContiguousVoxelPath

task() - Method in class ExecutionArguments

Arguments to help specify the outputs from the experiment.

Task<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.task

Encapsulates some kind of processing to be performed on a set of inputs.

Task() - Constructor for class Task

TaskArguments - Class in org.anchoranalysis.experiment.arguments

Arguments that can further specify an experiment's task in addition to its bean specification.

TaskArguments() - Constructor for class TaskArguments

taskDirectory() - Method in class ExperimentExecutor

TaskFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path

SelectParam<Path> factory for tasks.

tasksFooter() - Method in class Resources

Footer-message used after "show tasks".

TaskSingleInputHelper - Class in org.anchoranalysis.test.experiment.task

Executes a task on a single-input outputting into a specific directory.

TaskStatistics - Class in org.anchoranalysis.experiment.task

Maintains statistics on the execution of a task (considering jobs in aggregate)

TaskStatistics(long, RunningSum, RunningSum) - Constructor for class TaskStatistics

TaskWithoutSharedState<T extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task

A particular type of task that doesn't share-state between running jobs

TaskWithoutSharedState() - Constructor for class TaskWithoutSharedState

TerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination

A condition on whether to terminate the optimization or continue with further steps.

TerminationCondition() - Constructor for class TerminationCondition

TerminationConditionListOr - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination

TerminationConditionListOr(TerminationCondition, TerminationCondition) - Constructor for class TerminationConditionListOr

TerminationConditionListOr() - Constructor for class TerminationConditionListOr

test(T) - Method in interface CheckedPredicate

Applies a predicate like with Predicate.test(T).

test(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in interface NeighborPredicate

Tests if a neighbor satisfies a condition.

test(Point3i, T, T, int, int) - Method in interface PredicateBufferBinary

Tests a voxel location in two buffers.

test(KernelPointCursor) - Method in interface PredicateKernelPointCursor

Whether the condition is satisfied for a particular point?

test(byte, byte) - Method in interface PredicateTwoBytes

Do the combination of two arguments fulfill the predicate?

test(double, double) - Method in interface DoubleBiPredicate

Considers the relationship between valueFirst and valueSecond.

test(double, double) - Method in class EqualTo

test(double, double) - Method in class GreaterThan

test(double, double) - Method in class GreaterThanEqualTo

test(double, double) - Method in class LessThan

test(double, double) - Method in class LessThanEqualTo

TestDataInitializeException - Exception in org.anchoranalysis.test

An exception thrown when test-data cannot be loaded.

TestDataInitializeException(String) - Constructor for exception TestDataInitializeException

Creates with a message only.

TestDataInitializeException(Throwable) - Constructor for exception TestDataInitializeException

Creates with a cause only.

TestDataLoadException - Exception in org.anchoranalysis.test

An exception thrown when test-data cannot be loaded.

TestDataLoadException(String) - Constructor for exception TestDataLoadException

Creates with a message only.

TestDataLoadException(Throwable) - Constructor for exception TestDataLoadException

Creates with a cause only.

TestLoader - Class in org.anchoranalysis.test

Loads test data, which is found at some location on the filesystem.

TestLoaderMarks - Class in org.anchoranalysis.test.experiment

TestLoaderMarks(TestLoader) - Constructor for class TestLoaderMarks

TextFile - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter

TextFile() - Constructor for class TextFile

TextFileAsIntegerFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report

TextFileAsIntegerFromManifest() - Constructor for class TextFileAsIntegerFromManifest

TextFileAsIntegerFromPath - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report

TextFileAsIntegerFromPath() - Constructor for class TextFileAsIntegerFromPath

TextFileMarksReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter

TextFileMarksReporter() - Constructor for class TextFileMarksReporter

TextFileMessageLogger - Class in org.anchoranalysis.experiment.log

Logs messages to a text-file.

TextFileMessageLogger(String, ErrorReporter) - Constructor for class TextFileMessageLogger

Constructs a logger that (always) writes messages to a text-file with a specific path.

TextFileMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class TextFileMessageLogger

Constructs a logger that (maybe) writes messages to a text-file, with a path based upon an output name applied to a OutputterChecked.

TextFileOutput - Class in org.anchoranalysis.io.generator.text

Utility for writing to a text-file at a particular path, but only if it is enabled.

TextFileOutput(String) - Constructor for class TextFileOutput

TextFileOutputter - Class in org.anchoranalysis.io.generator.text

Maybe creates a TextFileOutput based upon settings in a OutputterChecked.

TextFileReader - Class in org.anchoranalysis.io.manifest.file

TextStyle - Class in org.anchoranalysis.image.io.bean.stack.combine

The size and style of text as it should appear in an image.

TextStyle(double) - Constructor for class TextStyle

TextStyle() - Constructor for class TextStyle

TextureScore - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity

From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei

TextureScore() - Constructor for class TextureScore

ThreeChannels - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color

ThreeChannels() - Constructor for class ThreeChannels

ThreeColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color

Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.

ThreeColoredObjects() - Constructor for class ThreeColoredObjects

threshold() - Method in class RelationToConstant

threshold() - Method in class RelationToThreshold

The threshold-value.

threshold() - Method in class BinaryNotOffVoxels

threshold() - Method in class BinaryNotOnVoxels

threshold() - Method in class BinaryOffVoxels

threshold() - Method in class BinaryOnVoxels

threshold(VoxelsUntyped) - Method in class Thresholder

Like Thresholder.threshold(VoxelsUntyped) but using default binary-values.

threshold(VoxelsUntyped, BinaryValuesByte) - Method in class Thresholder

Like Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.

threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class Thresholder

Thresholds voxels (across a range of values) so that they have only binary range (i.e.

threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class ThresholderGlobal

threshold(RelationToThreshold) - Method in interface VoxelStatistics

Derives statistics only of the voxels that satisfy a condition, relative to a threshold.

threshold(RelationToThreshold) - Method in class VoxelStatisticsCombined

threshold(RelationToThreshold) - Method in class VoxelStatisticsFromHistogram

threshold(VoxelsUntyped, float, BinaryValuesByte, Optional<ObjectMask>, boolean) - Static method in class VoxelsThresholder

Applies thresholding to VoxelsUntyped.

threshold(DoublePredicate) - Method in class Histogram

Generates a new histogram containing only values that match a predicate.

threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class ThresholderAutoIJ

Threshold - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.

Threshold() - Constructor for class Threshold

threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class ThresholderSimpleFillHoles2D

ThresholdAgainstChannel - Class in org.anchoranalysis.plugin.image.bean.segment.binary

Thresholds each voxels by comparing against another channel that has per-voxel thresholds

ThresholdAgainstChannel() - Constructor for class ThresholdAgainstChannel

thresholdByte(Voxels<UnsignedByteBuffer>, int, BinaryValuesByte) - Static method in class VoxelsThresholder

Applies thresholding to Voxels of unsigned byte data type.

ThresholdConfidence - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce

Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.

ThresholdConfidence(double) - Constructor for class ThresholdConfidence

Creates with a minimum-confidence level.

ThresholdConfidence() - Constructor for class ThresholdConfidence

Thresholded - Class in org.anchoranalysis.plugin.mpp.bean.region

Thresholded() - Constructor for class Thresholded

ThresholdedFeature - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent

Only keeps objects whose feature-value satisfies a condition relative to a threshold.

ThresholdedFeature() - Constructor for class ThresholdedFeature

ThresholdedVolume - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent

Only keeps objects whose feature-value satisfies a condition relative to a threshold.

ThresholdedVolume() - Constructor for class ThresholdedVolume

Thresholder - Class in org.anchoranalysis.image.bean.threshold

Thresholds a voxels to create a binary-voxels

Thresholder() - Constructor for class Thresholder

ThresholderAutoIJ - Class in org.anchoranalysis.plugin.fiji.bean.threshold

ThresholderAutoIJ() - Constructor for class ThresholderAutoIJ

ThresholderGlobal - Class in org.anchoranalysis.image.bean.threshold

Performs global thresholding.

ThresholderGlobal() - Constructor for class ThresholderGlobal

ThresholderGlobal(CalculateLevel) - Constructor for class ThresholderGlobal

ThresholderSimpleFillHoles2D - Class in org.anchoranalysis.plugin.imagej.bean.threshold

ThresholderSimpleFillHoles2D() - Constructor for class ThresholderSimpleFillHoles2D

ThresholderSimpleFillHoles2D(int) - Constructor for class ThresholderSimpleFillHoles2D

thresholdFloat(Voxels<FloatBuffer>, float, BinaryValuesByte) - Static method in class VoxelsThresholder

Applies thresholding to Voxels of float data type.

ThresholdHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold

Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version.

ThresholdHistogram() - Constructor for class ThresholdHistogram

ThumbnailBatch<T> - Interface in org.anchoranalysis.plugin.image.thumbnail

Creates thumbnails for a particular batch of objects that can be calibrated to have similar properties (identical scale etc.)

thumbnailFor(Stack) - Method in class ScaleToSize

thumbnailFor(Stack) - Method in class ThumbnailFromStack

Creates a thumbnail for a stack

thumbnailFor(T) - Method in interface ThumbnailBatch

Creates a thumbnail for an element in the batch

ThumbnailFromObjects - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object

Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects

ThumbnailFromObjects() - Constructor for class ThumbnailFromObjects

ThumbnailFromStack - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack

Creates a thumbnail from a stack

ThumbnailFromStack() - Constructor for class ThumbnailFromStack

Tiff - Class in org.anchoranalysis.io.bioformats.bean.writer

Writes a stack to the filesystem as a TIFF using the Bioformats library.

Tiff() - Constructor for class Tiff

Default constructor.

Tiff - Class in org.anchoranalysis.io.imagej.bean.stack.writer

Writes a TIFF image using ImageJ.

Tiff() - Constructor for class Tiff

TiffTimeSeries - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter

TiffTimeSeries() - Constructor for class TiffTimeSeries

Tile - Class in org.anchoranalysis.image.bean.spatial.arrange

Tile() - Constructor for class Tile

TileRasters - Class in org.anchoranalysis.image.io.stack.input

TileWithLabels - Class in org.anchoranalysis.image.io.bean.stack.combine

TileWithLabels() - Constructor for class TileWithLabels

TimeIntervalNamer - Class in org.anchoranalysis.plugin.io.naming.interval

Derives a human-friendly name for a time-interval.

TimeIntervalNamer(ZoneOffset) - Constructor for class TimeIntervalNamer

TimeSequence - Class in org.anchoranalysis.image.io.stack.time

TimeSequence(Stack) - Constructor for class TimeSequence

TimeSequence() - Constructor for class TimeSequence

TimeSequenceSupplier - Interface in org.anchoranalysis.image.io.stack.input

TimestampPattern - Class in org.anchoranalysis.plugin.io.bean.file.pattern

Extracts a timestamp from a file-name if it exists.

TimestampPattern(String) - Constructor for class TimestampPattern

TimestampPattern() - Constructor for class TimestampPattern

timestamps() - Method in interface OpenedImageFile

The timestamps and file-attributes associated with the image.

timestamps() - Method in class OpenedMultiFile

TimeStyle - Enum in org.anchoranalysis.plugin.io.naming.interval

How to style a time in a file-name.

title() - Method in class ReportFeature

title() - Method in class ReportFeatureEvaluator

title() - Method in class ReportFeatureWrapError

title() - Method in class NumberMarksFromManifest

title() - Method in class ReportFeatureForManifestFileBase

title() - Method in class RootFilePathRegEx

toAll() - Method in interface VoxelsAssigner

Assigns to all the voxels

toArray() - Method in class UpdatableMarksList

toArray(T[]) - Method in class UpdatableMarksList

toArray() - Method in class Extent

Derives an three-element array with each dimension in the extent.

toArray() - Method in class Point2i

Converts the point to an array.

toArray() - Method in class Point3d

Converts the point to an array.

toArrayXY() - Method in class Point3d

Converts the X and Y dimensions of the point to an array.

toAWTColor() - Method in class RGBColorBean

Converts to a Color representation.

toAWTColor() - Method in class RGBColor

Converts to a Color representation.

toBoundingBox() - Method in class PointRange

Creates a BoundingBox to just cover the range of points that have been added.

toBoundingBoxNoCheck() - Method in class PointRange

Like PointRange.toBoundingBox() but if no points exist, an exception is not thrown.

toBox(BoundingBox) - Method in interface VoxelsAssigner

Assigns to only voxels inside a bounding-box

ToByte - Class in org.anchoranalysis.image.voxel.convert

Base class for conversion to unsigned 8-bit.

ToByte() - Constructor for class ToByte

ToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert

ToByte() - Constructor for class ToByte

ToByteNoScaling - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to an unsigned 8-bit buffer without scaling any values.

ToByteNoScaling() - Constructor for class ToByteNoScaling

ToByteScaleByMaxValue - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to an unsigned 8-bit buffer linearly scaling against the maximum constant value.

ToByteScaleByMaxValue(int) - Constructor for class ToByteScaleByMaxValue

Creates with the maximum-value which existing values are scaled against.

ToByteScaleByMinMaxValue - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to an unsigned 8-bit buffer scaling against a the minimum and maximum constant.

ToByteScaleByMinMaxValue(int, int) - Constructor for class ToByteScaleByMinMaxValue

Creates with the minimum- and maximum-values which existing values are scaled against.

ToByteScaleByType - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to a UnsignedByteBuffer scaling against the maximum value in each buffer.

ToByteScaleByType() - Constructor for class ToByteScaleByType

ToByteUpperLowerQuantileIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.convert

ToByteUpperLowerQuantileIntensity() - Constructor for class ToByteUpperLowerQuantileIntensity

toChannel(ImagePlus, Optional<Resolution>) - Static method in class ConvertFromImagePlus

Converts an ImagePlus to a Channel.

toCommandLineException() - Method in exception InvalidPathArgumentException

ToConsole - Class in org.anchoranalysis.experiment.bean.log

Logs messages to the console.

ToConsole() - Constructor for class ToConsole

ToDimensions - Class in org.anchoranalysis.plugin.image.bean.scale

Calculates a scaling-factor to make the source image have identical dimensions as dimensionsTarget.

ToDimensions(int, int) - Constructor for class ToDimensions

Create with specific lengths for X and Y dimensions.

ToDimensions(DimensionsProvider) - Constructor for class ToDimensions

Create with specific dimensions.

ToDimensions(DimensionsProvider, boolean) - Constructor for class ToDimensions

Create with specific dimensions and preserveAspectRatio.

ToDimensions() - Constructor for class ToDimensions

toEitherTwoObjects(ObjectMask, ObjectMask, BoundingBox) - Method in interface VoxelsAssigner

Sets voxels to a value if the position is on in either of two masks

toExtent() - Method in class SizeExtents

ToFloat - Class in org.anchoranalysis.image.core.channel.convert

Converts a Channel to have a voxel data type of FloatBuffer without scaling.

ToFloat() - Constructor for class ToFloat

Creates without scaling.

ToFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat

Base class for implementations of ConvertTo that convert to float buffers.

ToFloat() - Constructor for class ToFloat

ToFloatNoScaling - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to a FloatBuffer without scaling any values.

ToFloatNoScaling() - Constructor for class ToFloatNoScaling

ToMultiple - Class in org.anchoranalysis.experiment.bean.log

Rather than logging to one location, logs to multiple locations (from a list).

ToMultiple(LoggingDestination, LoggingDestination) - Constructor for class ToMultiple

Constructs a logger to two locations

ToMultiple() - Constructor for class ToMultiple

toObject(ObjectMask) - Method in interface VoxelsAssigner

Sets voxels in a box to a particular value if they match an object-mask

toObject(ObjectMask, BoundingBox) - Method in interface VoxelsAssigner

Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)

toObjectIf(ObjectMask, IntPredicate) - Method in interface VoxelsAssigner

Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate

toObjectWhile(ObjectMask, IntPredicate) - Method in interface VoxelsAssigner

Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate

toPath() - Method in class NamedFile

Like File.toPath().

toPhysicalArea(double) - Method in class UnitConverter

Converts an area from square voxels to square meters.

toPhysicalArea(double, String) - Method in class UnitConverter

Converts an area from square voxels to physical units.

toPhysicalDistance(double, DirectionVector) - Method in class UnitConverter

Converts a distance from voxels to meters.

toPhysicalDistance(double, DirectionVector, String) - Method in class UnitConverter

Converts a distance from voxels to physical units.

toPhysicalVolume(double) - Method in class UnitConverter

Converts a volume from cubic voxels to cubic meters.

toPhysicalVolume(double, String) - Method in class UnitConverter

Converts a volume from cubic voxels to physical units.

ToPixelizedExtracter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract

ToPixelizedExtracter() - Constructor for class ToPixelizedExtracter

toRGBColor() - Method in class RGBColorBean

The RGBColor associated with the bean.

toSet() - Method in class ObjectMaskStream

Converts to a HashSet.

ToShortNoScaling - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to an unsigned 16-bit buffer without scaling any values.

ToShortNoScaling() - Constructor for class ToShortNoScaling

ToShortScaleByType - Class in org.anchoranalysis.image.voxel.convert

Converts voxel buffers to an unsigned 16-bit buffer, scaling against the maximum value in each data-type.

ToShortScaleByType() - Constructor for class ToShortScaleByType

toStack(Mat) - Static method in class ConvertFromMat

Convert from an OpenCV Mat to a Stack.

toString() - Method in class ImageLabelAnnotation

toString() - Method in class CostMatrix

toString() - Method in class Found

toString() - Method in class NotFound

toString() - Method in class AnchorBean

By default, we use AnchorBean.describeBean() as the string representation of the bean.

toString() - Method in class AssignerMatchClass

toString() - Method in class NamedBean

toString() - Method in class RegExList

toString() - Method in class RegExSimple

toString() - Method in class EqualToBean

toString() - Method in class GreaterThanBean

toString() - Method in class GreaterThanEqualToBean

toString() - Method in class LessThanBean

toString() - Method in class LessThanEqualToBean

toString() - Method in class RelationBean

toString() - Method in class RelationToConstant

toString() - Method in class RGBColor

toString() - Method in exception AnchorRuntimeException

toString() - Method in class GraphWithoutPayload

toString() - Method in class GraphWithPayload

toString() - Method in class TypedEdge

toString() - Method in class IndexRangeNegative

toString() - Method in class CommonContext

toString() - Method in class TraversalResult

toString() - Method in class FilenameSplitExtension

toString() - Method in class SplitPath

toString() - Method in class TypedValue

toString() - Method in class InputTypesExpected

toString() - Method in class ParametersUnbound

toString() - Method in class JobDescription

toString() - Method in class Feature

toString() - Method in class ChildCacheName

toString() - Method in class FeatureInitialization

toString() - Method in class FeatureInputResults

toString() - Method in class FeatureCSVMetadata

toString() - Method in class CombinedName

toString() - Method in interface MultiName

The full name, including both directory and file part, as a string.

toString() - Method in class SimpleName

toString() - Method in class LabelledResultsVector

toString() - Method in class FeatureNameList

toString() - Method in class ResultsVector

toString() - Method in class SharedFeatures

toString() - Method in class BoundingBoxesOnPlane

toString() - Method in class SizeXY

toString() - Method in class AreaPhysical

toString() - Method in class AreaPixels

toString() - Method in class VolumePhysical

toString() - Method in class VolumeVoxels

toString() - Method in class Channel

A string representation of a histogram of voxel-intensities in the channel.

toString() - Method in class Dimensions

toString() - Method in class Resolution

toString() - Method in class OverlappingObject

toString() - Method in class MatchedObject

toString() - Method in class ObjectCollectionWithProperties

toString() - Method in class ObjectWithProperties

toString() - Method in class NamedFeatureCalculatorMulti

toString() - Method in class FeatureInputPairObjects

toString() - Method in class FeatureInputSingleObject

toString() - Method in class ImageTimestampsAttributes

toString() - Method in class StackWriteAttributes

A user-friendly description of the stack-type to include in error and warning messages.

toString() - Method in class StackSeries

toString() - Method in class BinaryVoxels

toString() - Method in class BoundedVoxels

toString() - Method in class UnsignedBufferAsInt

Print a description and the the first {link #MAX_NUMBER_ROWS_COLUMNS_IN_TO_STRING} rows and columns as values.

toString() - Method in class VoxelBuffer

toString() - Method in class VoxelDataType

toString() - Method in class KernelApplicationParameters

toString(boolean, boolean) - Method in class ObjectCollection

A string representation of all objects in the collection using their center of gravities (and optionally indices).

toString() - Method in class ObjectCollection

Default string representation of the collection, one line with each object described by its center-of-gravity.

toString() - Method in class ObjectMask

A string representation of the object-mask showing: the center-of-gravity.

toString() - Method in class Voxels

Print a description and the the first {link #MAX_NUMBER_ROWS_COLUMNS_IN_TO_STRING} rows and columns as values.

toString() - Method in class ImageFileEncoding

toString() - Method in class ImageFileShape

toString() - Method in class OptionalNameValue

toString() - Method in class BoundOutputter

toString() - Method in class FileNamerContext

toString() - Method in class NamedFile

toString() - Method in class SingleFileInputBase

toString() - Method in class InputsWithDirectory

toString() - Method in class GlobExtractor.GlobWithDirectory

toString() - Method in class DualPathPredicates

toString() - Method in class PathMatchConstraints

toString() - Method in class FileType

toString() - Method in class ManifestDescription

toString() - Method in class OutputterTarget

toString() - Method in class Outputter

toString() - Method in class NamedPath

toString() - Method in class HelpConfig

toString() - Method in class QuadraticEquationSolver.QuadraticRoots

toString() - Method in class Histogram

A string representation of what's in the histogram.

toString() - Method in class MeanScale

toString() - Method in class EigenvalueAndVector

toString() - Method in class ResolvedBound

toString() - Method in class RegionMembership

toString() - Method in class RegionMembershipWithFlags

toString() - Method in class EnergyPair

toString() - Method in class EnergyTotal

toString() - Method in class MarksWithEnergyBreakdown

toString() - Method in class VoxelizedMarksWithEnergy

toString() - Method in class EnergySavedPairs

toString() - Method in class FeatureInputPairMemo

toString() - Method in class ColoredMarksWithDisplayStack

toString() - Method in class MarksWithDisplayStack

toString() - Method in class Circle

toString() - Method in class Ellipse

toString() - Method in class Ellipsoid

toString() - Method in class Sphere

toString() - Method in class Mark

String representation of the Mark.

toString() - Method in class MarkCollection

toString() - Method in class LineSegment

toString() - Method in class PointList

toString() - Method in class Polygon

toString() - Method in class PolygonCurve

toString() - Method in class RotatableBoundingBox

toString() - Method in class IdentifiablePair

toString() - Method in class PairPxlMarkMemo

toString() - Method in class ErrorNodeImpl

toString() - Method in class ProposerContext

toString() - Method in class KernelProposer

toString() - Method in class DualStack

toString() - Method in class AggIDCounter

toString() - Method in class Aggregator

toString() - Method in class FeedbackBeginParameters

toString() - Method in class FeedbackEndParameters

toString() - Method in class KernelWithIdentifier

toString() - Method in class WeightedKernel

toString() - Method in class ColoredOverlayCollection

toString() - Method in class ObjectDrawAttributes

toString() - Method in class AxisLimits

toString() - Method in class ObjectsToCompare

toString() - Method in class CalculateObjectMask

toString() - Method in class CalculateShellObjectMask

toString() - Method in class ObjectVertex

toString() - Method in class ChangeableOutputSequence

toString() - Method in class FeatureExporterContext

toString() - Method in class InitializationWithEnergyStack

toString() - Method in class LabelledResultsVectorWithThumbnail

toString() - Method in class ResultsVectorWithThumbnail

toString() - Method in class NamedChannel

toString() - Method in class ImageCSVLabellerInitialization

toString() - Method in class ImageLabellerStringMapInitialization

toString() - Method in class CopyContext

toString() - Method in class FileDetails

toString() - Method in class AnonymizeSharedState

toString() - Method in class IndexedRegionBase

toString() - Method in class SelectSlicesWithIndexBase

toString() - Method in class DistanceIndex

toString() - Method in class DistanceIndexTwice

toString() - Method in class ContiguousVoxelPath

toString() - Method in class LoopablePoints

toString() - Method in class ConvertedInput

toString() - Method in class KernelDeath.MarkAnd

toString() - Method in class PartitionedMarks

toString() - Method in class ToVoxelized

toString() - Method in class FitResult

toString() - Method in class ObjectWithEllipse

toString() - Method in class BoundingBox

toString() - Method in class Extent

toString() - Method in class Orientation2D

toString() - Method in class Orientation3DEulerAngles

toString() - Method in class OrientationAxisAngle

toString() - Method in class RotationMatrix

toString() - Method in class Point2d

toString() - Method in class Point2f

toString() - Method in class Point2i

toString() - Method in class Tuple3d

toString() - Method in class Tuple3f

toString() - Method in class Tuple3i

toString() - Method in class ScaleFactor

toStringUnixStyle(Path) - Static method in class FilePathToUnixStyleConverter

Converts a path to a string using Unix-style separators (forward-slashes).

toStringUnixStyle(String) - Static method in class FilePathToUnixStyleConverter

Converts a path to a string using Unix-style separators (forward-slashes).

ToSuggested - Class in org.anchoranalysis.plugin.image.bean.scale

Scales to the suggested-size if one is provided, otherwise calls fallback.

ToSuggested() - Constructor for class ToSuggested

total() - Method in class ResultsVector

The total value of all results.

totalAll(EnergyMemoList, EnergyStackWithoutParameters) - Method in class EnergySchemeWithSharedFeatures

TotalCount - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

TotalCount() - Constructor for class TotalCount

totalIndividual(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class EnergySchemeWithSharedFeatures

totalNumberSlices() - Method in class ImageFileShape

The total number of z-slices across all frames, channels.

ToTextFile - Class in org.anchoranalysis.experiment.bean.log

Logs to a text-file created in the output-directory under a particular name.

ToTextFile() - Constructor for class ToTextFile

ToTextFileBase - Class in org.anchoranalysis.experiment.bean.log

ToTextFileBase() - Constructor for class ToTextFileBase

ToTextFileOnlyIfFailure - Class in org.anchoranalysis.experiment.bean.log

Logs to a text file like with ToTextFile but the log is ONLY written if a failure occurs in the experiment.

ToTextFileOnlyIfFailure() - Constructor for class ToTextFileOnlyIfFailure

ToThePowerOfConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic

ToThePowerOfConstant() - Constructor for class ToThePowerOfConstant

TouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching

Base class for features that calculate touching with a dilated bounding box intersection

TouchingVoxels() - Constructor for class TouchingVoxels

ToUnsignedByte - Class in org.anchoranalysis.image.core.channel.convert

Converts a Channel to have a voxel data type of UnsignedByteBuffer (unsigned 8-bit) without scaling.

ToUnsignedByte() - Constructor for class ToUnsignedByte

Converting without scaling any values.

ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer>) - Constructor for class ToUnsignedByte

Convert with a particular VoxelsConverter.

ToUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Base class for implementations of ConvertTo that convert to unsigned byte buffers.

ToUnsignedByte() - Constructor for class ToUnsignedByte

ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.core.channel.convert

Converts a Channel to have a voxel data type of UnsignedByteBuffer (unsigned 8-bit) scaling from the range of the source data-type.

ToUnsignedByteScaleByMinMaxValue(int, int) - Constructor for class ToUnsignedByteScaleByMinMaxValue

Creates with the minimum- and maximum-values which existing values are scaled against.

ToUnsignedByteWithScaling - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Like ToUnsignedByte but applies scaling, if necessary, to map the original value to 8-bits.

ToUnsignedByteWithScaling(int) - Constructor for class ToUnsignedByteWithScaling

Create with the number of bits that are used in the input-type.

ToUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint

Base class for implementations of ConvertTo that convert to unsigned int buffers.

ToUnsignedInt() - Constructor for class ToUnsignedInt

ToUnsignedShort - Class in org.anchoranalysis.image.core.channel.convert

Converts a Channel to have a voxel data type of UnsignedShortBuffer.

ToUnsignedShort() - Constructor for class ToUnsignedShort

Converting without scaling any values.

ToUnsignedShort(VoxelsConverter<UnsignedShortBuffer>) - Constructor for class ToUnsignedShort

Convert with a particular VoxelsConverter.

ToUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort

Base class for implementations of ConvertTo that convert to unsigned short buffers.

ToUnsignedShort() - Constructor for class ToUnsignedShort

toVoxel(Point3i) - Method in interface VoxelsAssigner

Assigns one particular voxel

toVoxel(int, int, int) - Method in interface VoxelsAssigner

Assigns one particular voxel

toVoxelBuffer(Mat, Extent) - Static method in class VoxelBufferFromMat

Converts a Mat to a VoxelBuffer.

ToVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization

Before and after state, when a src is coverted in a VoxelizedMarksWithEnergy

ToVoxelized(T, VoxelizedMarksWithEnergy) - Constructor for class ToVoxelized

toVoxels(ImagePlus) - Static method in class ConvertFromImagePlus

Converts an ImagePlus to a VoxelsUntyped.

trackCurrentChild() - Method in class ProgressMultiple

Creates a progress-tracker for the current child.

transferCount(int, int) - Method in class Histogram

Moves all count for a particular value and adds it to the count for another.

transform(Assignment<ObjectMask>) - Method in class AssignmentGenerator

transform(ColorList) - Method in class ColorSchemeUnary

Transform an existing ColorList.

transform(ColorList) - Method in class Prepend

transform(ColorList) - Method in class Repeat

transform(ColorList) - Method in class Shuffle

transform(Channel) - Method in class ChannelGenerator

transform(ObjectCollection) - Method in class ObjectsAsUniqueValueGenerator

transform(ObjectCollection) - Method in class ObjectsMergedAsMaskGenerator

transform(ObjectMask) - Method in class ObjectAsMaskGenerator

transform(ObjectCollectionWithProperties) - Method in class ObjectsAsRGBGenerator

transform(BoundedList<ObjectMask>) - Method in class DrawObjectOnStackGenerator

transform(BoundingBox) - Method in class ExtractBoundingBoxAreaFromStackGenerator

transform(T) - Method in class RasterGeneratorBridge

transform(T) - Method in class RasterGeneratorDelegateToDisplayStack

transform(T) - Method in class RasterGeneratorDelegateToRaster

transform(Stack) - Method in class StackGenerator

transform(T) - Method in class OneStageGenerator

transform(T) - Method in class SingleFileTypeGeneratorBridge

transform(T) - Method in interface TransformingGenerator

Applies any necessary preprocessing to create an element suitable for writing to the filesystem.

transform(T) - Method in class TransformingGeneratorBridge

transform(List<File>, boolean) - Method in class FilesProviderUnary

Transform an existing collection of files.

transform(List<File>) - Method in class FilesProviderWithDirectoryUnary

Transform an existing collection of files.

transform(MarkCollection) - Method in class MarksAsUniqueValueGenerator

transform(ColoredMarksWithDisplayStack) - Method in class MarksGeneratorBase

transform(StateTransformer<T, S>, TransformationContext) - Method in class DualState

transform(S, TransformationContext) - Method in class Compose

transform(W, TransformationContext) - Method in interface StateTransformer

transform(List<File>, boolean) - Method in class Limit

transform(List<File>) - Method in class LimitWithDirectory

transform(List<File>, boolean) - Method in class RandomOrder

transform(List<File>, boolean) - Method in class RemoveMatching

transform(List<File>) - Method in class SampleWithDirectory

transform(List<File>, boolean) - Method in class SortAlphabetically

transform(List<File>) - Method in class SortAlphabeticallyWithDirectory

transform(List<File>, boolean) - Method in class FilterForExistingFiles

transform(VoxelizedMarksWithEnergy, TransformationContext) - Method in class AddDualTransformer

transform(DualVoxelizedMarks, TransformationContext) - Method in class RetrieveDestinationFromDual

transform(DualVoxelizedMarks, TransformationContext) - Method in class RetrieveSourceFromDual

transform(MarksFromPartition, TransformationContext) - Method in class RemovePartition

transform(MarksFromPartition, TransformationContext) - Method in class RemovePartitionAndThen

transform(MarkCollection, TransformationContext) - Method in class PointsFitter

transform(MarkCollection, TransformationContext) - Method in class AddEnergy

transform(ToVoxelized<T>, TransformationContext) - Method in class RetrieveDestinationFromVoxelized

transform(ToVoxelized<T>, TransformationContext) - Method in class RetrieveSourceFromVoxelized

transform(T, TransformationContext) - Method in class VoxelizeWithTransform

transform(Optional<W>, TransformationContext) - Method in class TransformMapOptional

TransformationAssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode

Applies a transformation to the kernel-type U to calculate the Energy used as the primary readout during optimization

TransformationAssignMode() - Constructor for class TransformationAssignMode

TransformationContext - Class in org.anchoranalysis.mpp.segment.transformer

TransformationContext(Dimensions, KernelCalculationContext, Logger) - Constructor for class TransformationContext

TransformingGenerator<T,S> - Interface in org.anchoranalysis.io.generator

Performs preprocessing to transform the element into another type before being written to the filesystem.

TransformingGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator

Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.

TransformingGeneratorBridge(TransformingGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class TransformingGeneratorBridge

TransformMapOptional<W,X> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization

TransformMapOptional(StateTransformer<W, X>) - Constructor for class TransformMapOptional

transpose() - Method in class RotationMatrix

Transposes the matrix immutably.

TraversalResult - Class in org.anchoranalysis.core.progress

The subdirectories and files found after traversing a directory on the file-system.

TraversalResult(List<Path>, List<Path>, int) - Constructor for class TraversalResult

traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class TraverseOuterContourOnImage

traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class TraverseOuterCounter

TraverseContourException - Exception in org.anchoranalysis.plugin.mpp.bean.contour

TraverseContourException(String) - Constructor for exception TraverseContourException

TraverseContourException(String, Throwable) - Constructor for exception TraverseContourException

TraverseDirectoryForProgress - Class in org.anchoranalysis.core.progress

Traverses files and subdirectories contained in a directory, in a way that is useful for tracking progress of processing algorithms that operate on each file.

traverseGlobal(Point3i, Consumer<Point3i>) - Method in class ContourTraverser

Traverse contourToTraverse using global-coordinates.

traverseNotRecursive(Path, Predicate<Path>) - Static method in class TraverseDirectoryForProgress

Traverses the subdirectories in path without any recursion into further sub-directories.

TraverseOuterContourOnImage - Class in org.anchoranalysis.plugin.mpp.bean.contour

Implementation of TraverseOuterCounter that uses a VisitScheduler for determining which pixels are traversed.

TraverseOuterContourOnImage() - Constructor for class TraverseOuterContourOnImage

TraverseOuterCounter - Class in org.anchoranalysis.plugin.mpp.bean.contour

Traverses the pixels on the exterior outer contour of an ObjectMask.

TraverseOuterCounter() - Constructor for class TraverseOuterCounter

TraversePointsOnContour - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation

TraversePointsOnContour() - Constructor for class TraversePointsOnContour

traverseRecursive(Path, int, Predicate<Path>, int) - Static method in class TraverseDirectoryForProgress

Performs a breadth-first traversal of the subdirectories of a path recursively until we get at least minNumberDirectories on a given level.

trigger() - Method in class TriggerTerminationCondition

trigger(Reporting<T>) - Method in class AggregateTriggerBank

TriggerTerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination

TriggerTerminationCondition() - Constructor for class TriggerTerminationCondition

Tuple3d - Class in org.anchoranalysis.spatial.point

A three-dimensional tuple of double values.

Tuple3d() - Constructor for class Tuple3d

Tuple3f - Class in org.anchoranalysis.spatial.point

A three-dimensional tuple of float values.

Tuple3f() - Constructor for class Tuple3f

Tuple3i - Class in org.anchoranalysis.spatial.point

A three-dimensional tuple of int values.

Tuple3i() - Constructor for class Tuple3i

twoNonOverlappingCircles(boolean) - Static method in class FeatureInputOverlappingCircleFixture

Two object-masks of circles in different locations WITHOUT any overlap.

twoOverlappingCircles(boolean) - Static method in class FeatureInputOverlappingCircleFixture

Two object-masks of circles in different locations WITH some overlap.

TwoVoxelMappingBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider

Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels

TwoVoxelMappingBase(IntBinaryOperation) - Constructor for class TwoVoxelMappingBase

TypedEdge<V,P> - Class in org.anchoranalysis.core.graph

An edge that exists in a graph, together with the two vertices that it connects.

TypedEdge(P, V, V) - Constructor for class TypedEdge

TypedValue - Class in org.anchoranalysis.core.value

A union of two types, either String or a numeric-value.

TypedValue(String) - Constructor for class TypedValue

Creates for a String value.

TypedValue(int) - Constructor for class TypedValue

Creates for an int value.

TypedValue(double, int) - Constructor for class TypedValue

Creates for an double value.

TypedValue(double) - Constructor for class TypedValue

Creates for an double value.

TypedValue(String, boolean) - Constructor for class TypedValue

U

UnaryWithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider

UnaryWithChannelBase() - Constructor for class UnaryWithChannelBase

UnaryWithMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask

UnaryWithMaskBase() - Constructor for class UnaryWithMaskBase

UnaryWithObjectsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider

UnaryWithObjectsBase() - Constructor for class UnaryWithObjectsBase

UnaryWithValueBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider

A ChannelProviderUnary which has a scalar value field

UnaryWithValueBase() - Constructor for class UnaryWithValueBase

unassigned(boolean) - Method in interface Assignment

The items that are not paired for a particular set.

unassigned(boolean) - Method in class ObjectVoxelIntersection

unassigned(boolean) - Method in class OverlappingObjects

UnchangedBase - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination

Parent class for TerminationCondition that rely on some attribute remaining unchanged for a certain number of iterations.

UnchangedBase() - Constructor for class UnchangedBase

UnchangedScore - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination

Terminate when the score remains unchanged for a certain number of iterations.

UnchangedScore() - Constructor for class UnchangedScore

UnchangedSize - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination

Terminate when the size remains unchanged for a certain number of iterations.

UnchangedSize() - Constructor for class UnchangedSize

unconvertedDataType() - Method in class DisplayStack

The data-type of the underlying voxels before they are converted to 8-bit.

underlyingBytes() - Method in class VoxelBuffer

An array of bytes that underlies the buffer (and can be written into a file).

uniform3D(int, int) - Static method in class BoundingBoxFactory

Short-hand factory method for creating a 3D bounding-box, where a coordinate is identical in each dimension.

UniformProposal<S,V> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme

Repeatedly propose new collections of marks and take the collection with optimal energy.

UniformProposal() - Constructor for class UniformProposal

UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection

UniformRandom() - Constructor for class UniformRandom

UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position

UniformRandom() - Constructor for class UniformRandom

UniformRandomRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii

UniformRandomRadiiProposer() - Constructor for class UniformRandomRadiiProposer

UniformRandomRadiiProposer(Bound, boolean) - Constructor for class UniformRandomRadiiProposer

union() - Method in class BoundingBox

For performing a union between this bounding-box and another.

uniqueIdentifierFor(T) - Method in class CombineObjectsForFeatures

Generates a unique identifier for a particular input

uniqueIdentifierFor(FeatureInputSingleObject) - Method in class EachObjectIndependently

uniqueIdentifierFor(FeatureInputPairObjects) - Method in class PairNeighbors

uniquelyIdentifyAllProperties() - Method in class MorphologicalIterations

A string that uniquely identifies all properties in the bean, but NOT friendly to humans

uniqueName() - Method in interface GenerateUniqueParameterization

A string describing this class and all its parameterization.

uniqueName() - Method in class RelationBean

uniqueName() - Method in class RelationToConstant

uniqueName() - Method in class BinaryVoxelsBase

uniqueName() - Method in class CenterSliceWindow

uniqueName() - Method in class GreatestAreaSlice

uniqueName() - Method in class IndexedRegionBase

uniqueName() - Method in class SelectSlicesBase

uniqueName() - Method in class SelectSlicesWithIndexBase

uniqueName() - Method in class Thresholded

unitArea() - Method in class Resolution

Multiplying the X- and Y- resolution values together.

unitConvert() - Method in class Dimensions

Converts voxel-scaled measurements to/from physical units.

unitConvert() - Method in class Resolution

Converts voxelized measurements to/from physical units.

UnitConverter - Class in org.anchoranalysis.image.core.dimensions

Converts from voxelized units to different physical measurements of area / volume / distance.

UnitConverter(Resolution) - Constructor for class UnitConverter

UnitConverter - Class in org.anchoranalysis.plugin.mpp.feature.bean.unit

Converts units (distance, area, volume) to a another representation (e.g.

UnitConverter() - Constructor for class UnitConverter

unitConvertOptional() - Method in class MergeBase

UnitsWithinRange<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.plugin.image.feature.bean.physical

Checks if a value lies within a range defined by units (a minimum and maximum boundary)

UnitsWithinRange() - Constructor for class UnitsWithinRange

UnitTestCompareUtilities - Class in org.anchoranalysis.test.experiment.launcher

UnitValueArea - Class in org.anchoranalysis.image.bean.unitvalue.extent.area

UnitValueArea() - Constructor for class UnitValueArea

UnitValueArea(double) - Constructor for class UnitValueArea

UnitValueAreaOrVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent

UnitValueAreaOrVolume() - Constructor for class UnitValueAreaOrVolume

UnitValueDistance - Class in org.anchoranalysis.image.bean.unitvalue.distance

UnitValueDistance() - Constructor for class UnitValueDistance

UnitValueException - Exception in org.anchoranalysis.image.bean.nonbean.error

UnitValueException(String) - Constructor for exception UnitValueException

UnitValueException(Exception) - Constructor for exception UnitValueException

UnitValueVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume

UnitValueVolume() - Constructor for class UnitValueVolume

unitVolume() - Method in class Resolution

Multiplying the X- and Y- and Z- resolution values together.

UnsignedBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive

Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO Buffer.

UnsignedBuffer(Buffer) - Constructor for class UnsignedBuffer

UnsignedBufferAsInt - Class in org.anchoranalysis.image.voxel.buffer.primitive

A UnsignedBuffer that exposes its internal types as int.

UnsignedBufferAsInt(Buffer) - Constructor for class UnsignedBufferAsInt

Construct with a delegate buffer.

unsignedByteArray(byte[]) - Static method in class VoxelBufferWrap

Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.

UnsignedByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive

Wraps a ByteBuffer but automatically performs conversion to int.

unsignedByteBuffer(UnsignedByteBuffer) - Static method in class VoxelBufferWrap

Wraps an unsigned-byte buffer into a voxel-buffer.

UnsignedByteFromFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Converts a ByteBuffer encoding a float type to unsigned byte type, as expected in an Anchor VoxelBuffer.

UnsignedByteFromFloat() - Constructor for class UnsignedByteFromFloat

unsignedByteFromMat(Mat, Extent) - Static method in class VoxelBufferFromMat

Converts a Mat to a VoxelBuffer with voxel data-type UnsignedByteBuffer.

UnsignedByteFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Like ToUnsignedByte and provides common functionality when converting to an unsigned byte.

UnsignedByteFromUnsignedByte() - Constructor for class UnsignedByteFromUnsignedByte

UnsignedByteFromUnsignedByteInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Converts a ByteBuffer encoding unsigned bytes (with interleaving) to unsigned byte type, as expected in an Anchor VoxelBuffer.

UnsignedByteFromUnsignedByteInterleaving() - Constructor for class UnsignedByteFromUnsignedByteInterleaving

UnsignedByteFromUnsignedByteNoInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Converts a ByteBuffer encoding unsigned bytes (no interleaving) to unsigned byte type, as expected in an Anchor VoxelBuffer.

UnsignedByteFromUnsignedByteNoInterleaving() - Constructor for class UnsignedByteFromUnsignedByteNoInterleaving

UnsignedByteFromUnsignedByteNoInterleavingScale - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Converts data of type unsigned byte to unsigned byte.

UnsignedByteFromUnsignedByteNoInterleavingScale(int) - Constructor for class UnsignedByteFromUnsignedByteNoInterleavingScale

Create with a number of effective-bits.

UnsignedByteFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Converts data of type unsigned int to unsigned byte.

UnsignedByteFromUnsignedInt(int) - Constructor for class UnsignedByteFromUnsignedInt

Create with a number of effective-bits.

UnsignedByteFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Converts data of type unsigned short to unsigned byte.

UnsignedByteFromUnsignedShort(int) - Constructor for class UnsignedByteFromUnsignedShort

Create with a number of effective-bits.

unsignedByteRaw(ByteBuffer) - Static method in class VoxelBufferWrap

Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.

unsignedByteToInt(byte) - Static method in class PrimitiveConverter

Converts an unsigned-byte value to a signed int.

unsignedByteToShort(byte) - Static method in class PrimitiveConverter

Converts an unsigned-byte value to a signed short.

UnsignedByteVoxelType - Class in org.anchoranalysis.image.voxel.datatype

A 8-bit voxel data-type representing unsigned-byte numbers.

unsignedIntArray(int[]) - Static method in class VoxelBufferWrap

Wraps an unsigned-int buffer into a voxel-buffer.

UnsignedIntBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive

Wraps an IntBuffer but automatically performs conversion to long.

unsignedIntBuffer(UnsignedIntBuffer) - Static method in class VoxelBufferWrap

Wraps an unsigned-int buffer (represented by a NIO signed-buffer) into a voxel-buffer.

UnsignedIntFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint

UnsignedIntFromUnsignedInt() - Constructor for class UnsignedIntFromUnsignedInt

unsignedIntToInt(int) - Static method in class PrimitiveConverter

Converts an unsigned-int value to a signed int.

unsignedIntToLong(int) - Static method in class PrimitiveConverter

Converts an unsigned-int value to a signed long.

unsignedIntToShort(int) - Static method in class PrimitiveConverter

Converts an unsigned-int value to a signed int.

UnsignedIntVoxelType - Class in org.anchoranalysis.image.voxel.datatype

A 32-bit voxel data-type representing unsigned-int numbers.

unsignedShortArray(short[]) - Static method in class VoxelBufferWrap

Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.

UnsignedShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive

Wraps a ShortBuffer but automatically performs conversion to int.

unsignedShortBuffer(UnsignedShortBuffer) - Static method in class VoxelBufferWrap

Wraps an unsigned-short buffer into a voxel-buffer.

unsignedShortFromMat(Mat, Extent) - Static method in class VoxelBufferFromMat

Converts a Mat to a VoxelBuffer with voxel data-type UnsignedShortBuffer.

UnsignedShortFromSignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort

UnsignedShortFromSignedShort() - Constructor for class UnsignedShortFromSignedShort

UnsignedShortFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort

UnsignedShortFromUnsignedShort() - Constructor for class UnsignedShortFromUnsignedShort

unsignedShortRaw(ShortBuffer) - Static method in class VoxelBufferWrap

Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.

unsignedShortToInt(short) - Static method in class PrimitiveConverter

Converts an unsigned-short value to a signed int.

UnsignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype

A 16-bit voxel data-type representing unsigned-short numbers.

UnsignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype

Base class for voxel-data-types that are unsigned and integral.

UnsignedVoxelType(int, String, long) - Constructor for class UnsignedVoxelType

Construct for a particular number of bits, with a unique identifier, and with bounds on the values.

UnsupportedMarkTypeException - Exception in org.anchoranalysis.mpp.mark

UnsupportedMarkTypeException(String) - Constructor for exception UnsupportedMarkTypeException

UnsupportedMarkTypeException(Exception) - Constructor for exception UnsupportedMarkTypeException

untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer>, byte) - Static method in class IterateVoxelsEqualTo

Iterates each voxel until a specific intensity value is found.

UpdatableBeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition

Rather than checking if obj1 vs obj2 is accepted instead there's a two stage process

UpdatableMarks - Interface in org.anchoranalysis.mpp.mark

UpdatableMarksList - Class in org.anchoranalysis.mpp.feature.mark

UpdatableMarksList() - Constructor for class UpdatableMarksList

update(int) - Method in interface Progress

Informs the tracker of an update in the progress.

update(int) - Method in class ProgressConsole

update(int) - Method in class ProgressIgnore

update() - Method in class ProgressIncrement

Informs the tracker of an update in the progress.

update(double) - Method in class ProgressMultiple

Informs the tracker of an update in the progress of the current child tracker.

update(Integer) - Method in class IncreasingIntegers

update(Integer) - Method in class IncrementingIntegers

update(T) - Method in class SequenceType

update(String) - Method in class StringsWithoutOrder

update(Point2d, Point2d, Orientation) - Method in class RotatableBoundingBox

updateAfterAcceptance(S, T, T) - Method in class Kernel

If the kernel is accepted, makes the necessary changes to a ListUpdatableMarkSetCollection

updateAfterAcceptance(UpdatableMarksList, MarksFromPartition, MarksFromPartition) - Method in class KernelBirthPartition

updateAfterAcceptance(UpdatableMarksList, MarksFromPartition, MarksFromPartition) - Method in class KernelDeathPartition

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelBirthAndKill

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelExchange

updateAfterAcceptance(UpdatableMarksList, MarksFromPartition, MarksFromPartition) - Method in class KernelInitialMarksFromPartition

updateAfterAcceptance(UpdatableMarksList, MarkCollection, MarkCollection) - Method in class KernelInitialMarksProposed

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelInitialMarksVoxelized

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelMerge

updateAfterAcceptance(UpdatableMarksList, T, T) - Method in class KernelReplace

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelSplit

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelBirthVoxelized

updateAfterAcceptance(UpdatableMarksList, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class KernelDeathVoxelized

updateAfterMarkChange() - Method in class Ellipsoid

updateAfterPointsChange() - Method in class PointList

updateAfterPointsChange() - Method in class PointListBase

updateAfterPointsChange() - Method in class Polygon

updateIndex(String, int) - Method in class SequenceMemory

updateLabeling(double) - Method in class HungarianAlgorithm

Update labels with the specified slack by adding the slack value for committed workers and by subtracting the slack value for committed jobs.

UpdateMarkSetException - Exception in org.anchoranalysis.mpp.mark

UpdateMarkSetException(String) - Constructor for exception UpdateMarkSetException

UpdateMarkSetException(Exception) - Constructor for exception UpdateMarkSetException

updateshell(double) - Method in class Ellipse

updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class AndCondition

updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class NeighborhoodCondition

updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in interface UpdatableBeforeCondition

updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class WrapAsUpdatable

updateTotal(EnergyMemoList, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown

UpperLowerQuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel

Converts a Channel to UnsignedByteBuffer by scaling against lower and upper quantiles of the intensity values that appear in it.

UpperLowerQuantileIntensity(double, double) - Constructor for class UpperLowerQuantileIntensity

Scale with quantile values for the lower and upper boundaries.

UpperLowerQuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram

Converts a Channel to UnsignedByteBuffer by scaling against lower and upper quantiles of the intensity values from a corresponding histogram.

UpperLowerQuantileIntensityFromHistogram(double, double) - Constructor for class UpperLowerQuantileIntensityFromHistogram

Scale with quantile values for the lower and upper boundaries - without any scaling factors.

UpperLowerQuantileIntensityFromHistogram(double, double, double, double) - Constructor for class UpperLowerQuantileIntensityFromHistogram

Scale with quantile values for the lower and upper boundaries - with explicit scaling factors.

URL_OUTPUT_OPTIONS - Static variable in class AnchorWebsiteLinks

A URL for showing command-line options relating to outputting.

URL_PREDEFIEND_TASKS - Static variable in class AnchorWebsiteLinks

A URL for showing predefined tasks that can be used.

usageFooter() - Method in class Resources

Footer-message that describes usage.

usageHeader() - Method in class Resources

Header-message that describes usage.

useDefault() - Static method in class SelectParamFactory

Use default manager.

UseDefaultManager - Class in org.anchoranalysis.launcher.executor.selectparam

Uses whatever default-manager exists

UseDefaultManager() - Constructor for class UseDefaultManager

useDetailedLogging() - Method in class Experiment

Whether to detail more (a lengthy experiment) or less (something quick and simple - suitable for console)?

useDetailedLogging() - Method in class InputOutputExperiment

useDetailedLogging() - Method in class OutputExperiment

useDetailedLogging() - Method in class QuickExperiment

useDetailedLogging() - Method in class QuickMultiDatasetExperiment

useDetailedLogging() - Method in class QuickMultiDatasetStructuredExperiment

useElseInstead(int, int) - Method in class CalculateLevelRelativeToThreshold

Uses calculateLevelElse instead of the standard calculation-level approach

useElseInstead(int, int) - Method in class IfGreaterThan

useElseInstead(int, int) - Method in class IfLessThan

V

valueByDimension(int) - Method in class Resolution

A component of a resolution corresponding to a particular dimension by index.

valueByDimension(Axis) - Method in class Resolution

A component of the tuple corresponding to a particular axis.

valueByDimension(int) - Method in class Extent

The size in the dimension identified by dimensionIndex.

valueByDimension(Axis) - Method in class Extent

The size in the dimension identified by axis.

valueByDimension(Axis) - Method in interface ReadableTuple3i

A component of a tuple corresponding to a particular axis.

valueByDimension(int) - Method in interface ReadableTuple3i

A component of a tuple corresponding to a particular dimension by index.

valueByDimension(Axis) - Method in class Tuple3d

A component of the tuple corresponding to a particular axis.

valueByDimension(int) - Method in class Tuple3d

A component of the tuple corresponding to a particular dimension by index.

valueByDimension(Axis) - Method in class Tuple3f

A component of a tuple corresponding to a particular axis.

valueByDimension(int) - Method in class Tuple3f

A component of a tuple corresponding to a particular dimension by index.

valueByDimension(int) - Method in class Tuple3i

A component of a tuple corresponding to a particular dimension by index.

valueByDimension(Axis) - Method in class Tuple3i

valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects

valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class FeatureIntersectingObjectsSingleElement

valueFor(FeatureCalculationInput<FeatureInputSingleObject>, ResolvedPart<ObjectCollection, FeatureInputSingleObject>) - Method in class NumberIntersectingObjects

valueFor(Axis, int, int, int) - Static method in class AxisConverter

Multiplexes the a value corresponding to a particular axis.

valueFromFirst(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class FeatureDeriveFromPair

valueFromMerged(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class FeatureDeriveFromPair

valueFromSecond(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class FeatureDeriveFromPair

valueOf(String) - Static method in enum ImageFileFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum NonImageFileFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ConversionPolicy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum OrientationChange

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum SpatialUnits.UnitSuffix

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum CalculateInputFromPair.Extract

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum StackRGBState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum OutsideKernelPolicy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum DateStyle

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum TimeStyle

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum Axis

Returns the enum constant of this type with the specified name.

values() - Static method in enum ImageFileFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum NonImageFileFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ConversionPolicy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum OrientationChange

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum SpatialUnits.UnitSuffix

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum CalculateInputFromPair.Extract

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum StackRGBState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum OutsideKernelPolicy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum DateStyle

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum TimeStyle

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum Axis

Returns an array containing the constants of this enum type, in the order they are declared.

variance() - Method in interface VoxelStatistics

The variance of all voxel values.

variance() - Method in class Histogram

Calculates the variance of the distribution represented by the histogram.

variance() - Method in class VarianceCalculatorDouble

Calculate the variance, based on the current state of running-sums.

variance() - Method in class VarianceCalculatorLong

Calculate the variance, based on the current state of running-sums.

Variance - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

Calculates the variance of all the values in the histogram.

Variance() - Constructor for class Variance

VarianceCalculatorDouble - Class in org.anchoranalysis.math.statistics

Calculates variance efficiently, as successive values are added, using double to store sums internally.

VarianceCalculatorDouble(double, double, long) - Constructor for class VarianceCalculatorDouble

VarianceCalculatorDouble() - Constructor for class VarianceCalculatorDouble

VarianceCalculatorLong - Class in org.anchoranalysis.math.statistics

Calculates variance efficiently, as successive values are added, using long to store sums internally.

VarianceCalculatorLong(long, long, long) - Constructor for class VarianceCalculatorLong

VarianceCalculatorLong() - Constructor for class VarianceCalculatorLong

VarianceFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments

VarianceFilter2D() - Constructor for class VarianceFilter2D

Vector3d - Class in org.anchoranalysis.spatial.point

A three-dimensional vector of double values.

Vector3d(Tuple3d) - Constructor for class Vector3d

Creates with the same values as an existing Tuple3d.

Vector3d(double, double, double) - Constructor for class Vector3d

Create with values for each dimension.

Vector3d() - Constructor for class Vector3d

VectorInDirection - Class in org.anchoranalysis.image.bean.spatial.direction

VectorInDirection(DirectionVector) - Constructor for class VectorInDirection

VectorInDirection() - Constructor for class VectorInDirection

VectorInDirection(double, double, double) - Constructor for class VectorInDirection

versionFooter() - Method in class Resources

Footer-message that accompanies a version message, if it exists.

versionFromMavenProperties() - Method in class Resources

Gets the current version of the software by reading a properties-file provided by the Maven build

vertices() - Method in class GraphWithoutPayload

The set of all vertices in the graph.

vertices() - Method in class GraphWithPayload

The set of all vertices in the graph.

verticesAsObjects() - Method in class MergeGraph

VeryBright - Class in org.anchoranalysis.bean.shared.color.scheme

Creates a list by repeating a defined constant list of very bright colors.

VeryBright() - Constructor for class VeryBright

VisitScheduler - Class in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler

VisitScheduler() - Constructor for class VisitScheduler

VisitSchedulerAnd - Class in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler

VisitSchedulerAnd() - Constructor for class VisitSchedulerAnd

VisitSchedulerConvexAboutRoot - Class in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler

VisitSchedulerConvexAboutRoot() - Constructor for class VisitSchedulerConvexAboutRoot

VisitSchedulerMaxDistanceAlongContour - Class in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler

VisitSchedulerMaxDistanceAlongContour() - Constructor for class VisitSchedulerMaxDistanceAlongContour

VisitSchedulerUniformSample - Class in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler

VisitSchedulerUniformSample() - Constructor for class VisitSchedulerUniformSample

VisualizeOnBackground - Class in org.anchoranalysis.plugin.mpp.bean.define

Adds a visualization for all binary-masks and object-collections that are added using a particular background

VisualizeOnBackground() - Constructor for class VisualizeOnBackground

volume(int) - Method in class Circle

volume(int) - Method in class Ellipse

volume(int) - Method in class Ellipsoid

volume(int) - Method in class Sphere

volume(int) - Method in class Mark

volume(int) - Method in class LineSegment

volume(int) - Method in class PointList

volume(int) - Method in class Polygon

volume(int) - Method in class PolygonCurve

volume(int) - Method in class RotatableBoundingBox

Volume<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions

Calculates the volume (x, y and z dimensions) of the scene from the dimensions

Volume() - Constructor for class Volume

Volume - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region

Volume() - Constructor for class Volume

volumeAgg(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class OverlapMaskBase

VolumeMin - Class in org.anchoranalysis.plugin.mpp.bean.check

VolumeMin() - Constructor for class VolumeMin

VolumePhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume

VolumePhysical() - Constructor for class VolumePhysical

volumeStatistic(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class OverlapMaskBase

VolumeVoxels - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume

VolumeVoxels() - Constructor for class VolumeVoxels

VolumeVoxels(double) - Constructor for class VolumeVoxels

voxel(int, int) - Method in interface VoxelsExtracter

Gets the value of one particular voxel.

voxel(int, int, int) - Method in interface VoxelsExtracter

Gets the value of one particular voxel.

voxel(ReadableTuple3i) - Method in interface VoxelsExtracter

Gets the value of one particular voxel.

VoxelBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer

A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.

VoxelBuffer() - Constructor for class VoxelBuffer

VoxelBufferFactory - Class in org.anchoranalysis.image.voxel.buffer

Creating voxel-buffers and arrays of voxel-buffers of various types.

VoxelBufferFromMat - Class in org.anchoranalysis.plugin.opencv.convert

Converts a Mat to a VoxelBuffer.

VoxelBufferUnsigned<T extends UnsignedBuffer> - Class in org.anchoranalysis.image.voxel.buffer

A parent class for VoxelBuffer that accepts unsigned-buffers and implements some common operations.

VoxelBufferUnsigned(T) - Constructor for class VoxelBufferUnsigned

Creates to reuse a particular buffer.

VoxelBufferWrap - Class in org.anchoranalysis.image.voxel.buffer

Wraps arrays and buffers of primitive-types into VoxelBuffer.

VoxelDataType - Class in org.anchoranalysis.image.voxel.datatype

The type of data that a single voxel represents in an image or related buffer.

VoxelDataType(int, String, long, long) - Constructor for class VoxelDataType

VoxelDataTypeFactoryMultiplexer<T> - Class in org.anchoranalysis.image.voxel.datatype

Multiplexes between factories for the various VoxelDataTypes.

VoxelDataTypeFactoryMultiplexer(T, T, T, T) - Constructor for class VoxelDataTypeFactoryMultiplexer

voxelized() - Method in class VoxelizedMarkMemo

A voxelized-respentation of the mark

VoxelizedMark - Interface in org.anchoranalysis.mpp.mark.voxelized

A voxelized representation of a Mark i.e.

VoxelizedMarkFactory - Class in org.anchoranalysis.mpp.mark.voxelized

VoxelizedMarkMemo - Class in org.anchoranalysis.mpp.mark.voxelized.memo

Memoization of retrieving a VoxelizedMark from a mark

VoxelizedMarkMemo(Mark, EnergyStackWithoutParameters, RegionMap) - Constructor for class VoxelizedMarkMemo

VoxelizedMarksChangeReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter

VoxelizedMarksChangeReporter() - Constructor for class VoxelizedMarksChangeReporter

VoxelizedMarksPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter

VoxelizedMarksPeriodicReporter() - Constructor for class VoxelizedMarksPeriodicReporter

VoxelizedMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks

A collection of marks, their voxelized equivalents, and associated energy.

VoxelizedMarksWithEnergy(MarksWithEnergyBreakdown, EnergyStack, SharedFeatures, Logger) - Constructor for class VoxelizedMarksWithEnergy

VoxelizedMarksWithEnergyFactory - Class in org.anchoranalysis.plugin.mpp.segment.optimization

VoxelizeWithTransform<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized

Converts a Marks to a MarksToPixelized using a transformer

VoxelizeWithTransform() - Constructor for class VoxelizeWithTransform

VoxelizeWithTransform(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Constructor for class VoxelizeWithTransform

VoxelPartition<T> - Interface in org.anchoranalysis.mpp.index

A partition of voxels-values by slice.

VoxelPartitionFactory<T> - Interface in org.anchoranalysis.mpp.index.factory

VoxelPartitionHistogram - Class in org.anchoranalysis.mpp.index

VoxelPartitionHistogram(int, Supplier<Histogram>) - Constructor for class VoxelPartitionHistogram

VoxelPartitonFactoryHistogram - Class in org.anchoranalysis.mpp.index.factory

VoxelPartitonFactoryHistogram() - Constructor for class VoxelPartitonFactoryHistogram

VoxelPhysicalSize<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions

The physical size of a pixel in a specific dimension.

VoxelPhysicalSize() - Constructor for class VoxelPhysicalSize

voxels() - Method in class Channel

The underlying voxels in the channel.

voxels() - Method in class Mask

The underlying voxels in the mask.

voxels() - Method in class BinaryVoxels

Voxels that should only have two intensity-values (representing on and off states).

voxels() - Method in class BoundedVoxels

Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).

voxels() - Method in class ObjectMask

The underlying voxel memory buffers for the object-mask, exposed via Voxels.

Voxels<T> - Class in org.anchoranalysis.image.voxel

A box (3-dimensions) with voxel-data.

Voxels(SliceBufferIndex<T>, VoxelsFactoryTypeBound<T>, VoxelsArithmetic) - Constructor for class Voxels

voxels() - Method in interface VoxelizedMark

voxels() - Method in class EncodedVoxels

VoxelsArithmetic - Interface in org.anchoranalysis.image.voxel.arithmetic

Allows manipulation of voxel intensities via arithmetic operations.

VoxelsArithmeticFactory - Class in org.anchoranalysis.image.voxel.arithmetic

Creates VoxelsArithmetic for buffers of different types.

VoxelsAssigner - Interface in org.anchoranalysis.image.voxel.assigner

Assigns values to some or all voxels.

VoxelsAssignerFactory - Class in org.anchoranalysis.image.voxel.assigner

Creates VoxelsAssigner for buffers of different types.

VoxelsConverter<T> - Class in org.anchoranalysis.image.voxel.convert

Converts voxels from one data-type to another.

VoxelsConverter() - Constructor for class VoxelsConverter

VoxelScore - Class in org.anchoranalysis.image.feature.bean

Calculates a per-voxel score.

VoxelScore() - Constructor for class VoxelScore

voxelsEqualTo(int) - Method in class Channel

Operations on whether particular voxels are equal to a particular value.

voxelsEqualTo(int) - Method in interface VoxelsExtracter

Operations on whether particular voxels are equal to a particular value.

VoxelsExtracter<T> - Interface in org.anchoranalysis.image.voxel.extracter

Provides methods to read/copy/duplicate regions of voxels.

VoxelsExtracterFactory - Class in org.anchoranalysis.image.voxel.extracter

Creates VoxelsExtracter corresponding to Voxels of differing data-type.

VoxelsFactory - Class in org.anchoranalysis.image.voxel.factory

Creates VoxelsUntyped and provides a singleton location for implementations of VoxelsFactoryTypeBound for different types.

VoxelsFactoryTypeBound<T> - Interface in org.anchoranalysis.image.voxel.factory

A factory for creating voxels with a particular buffer-type.

VoxelsFloat - Class in org.anchoranalysis.image.voxel

Implementation of Voxels whose voxels are of type float.

VoxelsFloat(SliceBufferIndex<FloatBuffer>) - Constructor for class VoxelsFloat

Create from a buffer, indexed by slice.

voxelsGreaterThan(int) - Method in class Channel

Operations on whether particular voxels are greater than a threshold (but not equal to).

voxelsGreaterThan(int) - Method in interface VoxelsExtracter

Operations on whether particular voxels are greater than a threshold (but not equal to).

voxelsMaximumIntensityProjection() - Method in interface VoxelizedMark

voxelsOff() - Method in class Mask

Operations on whether particular voxels are off.

voxelsOff() - Method in class ObjectMask

Provides a VoxelsPredicate that finds or counts all off voxels in the object-mask.

voxelsOn() - Method in class Mask

Operations on whether particular voxels are on.

voxelsOn() - Method in class ObjectMask

Provides a VoxelsPredicate that finds or counts all on voxels in the object-mask.

VoxelsPredicate - Interface in org.anchoranalysis.image.voxel.extracter.predicate

Methods to find or count voxels that satisfy a predicate.

VoxelStatistics - Interface in org.anchoranalysis.image.voxel.statistics

Allows retrieval of statistics about voxel values.

VoxelStatisticsCombined - Class in org.anchoranalysis.image.voxel.statistics

Aggregates statistics of a list of VoxelStatistics as if they were one.

VoxelStatisticsCombined() - Constructor for class VoxelStatisticsCombined

VoxelStatisticsFromHistogram - Class in org.anchoranalysis.image.voxel.statistics

Calculates statistics from a Histogram of voxel intensities.

VoxelStatisticsFromHistogram(Histogram) - Constructor for class VoxelStatisticsFromHistogram

VoxelsThresholder - Class in org.anchoranalysis.image.voxel.thresholder

Performs a thresholding operation on voxels.

VoxelsUnsignedByte - Class in org.anchoranalysis.image.voxel

Implementation of Voxels whose voxels are of type unsigned byte (8-bit).

VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer>) - Constructor for class VoxelsUnsignedByte

Create from a buffer, indexed by slice.

VoxelsUnsignedInt - Class in org.anchoranalysis.image.voxel

Implementation of Voxels whose voxels are of type unsigned int (32-bit).

VoxelsUnsignedInt(SliceBufferIndex<UnsignedIntBuffer>) - Constructor for class VoxelsUnsignedInt

Create from a buffer, indexed by slice.

VoxelsUnsignedShort - Class in org.anchoranalysis.image.voxel

Implementation of Voxels whose voxels are of type unsigned short (16-bit).

VoxelsUnsignedShort(SliceBufferIndex<UnsignedShortBuffer>) - Constructor for class VoxelsUnsignedShort

Create from a buffer, indexed by slice.

VoxelsUntyped - Class in org.anchoranalysis.image.voxel

Stores memory buffers representing image voxels, without explicit typing of buffers.

VoxelsUntyped(Voxels<?>) - Constructor for class VoxelsUntyped

Creates to wrap a Voxels of unspecified type.

voxelWithMaxIntensity() - Method in interface VoxelsExtracter

Finds the maximum-value of any voxel and rounds up (ceiling) to nearest long.

W

walk(UnsignedByteBuffer, BufferRetriever) - Method in class WalkPredicate

Do any neighboring voxels in any direction satisfy the predicate?

walk(UnsignedByteBuffer, BufferRetriever) - Method in class WalkRunnable

Walks in X and Y direction, and Z direction if enabled.

WalkPredicate - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel

Walks in X, Y and Z directions from a point, test a NeighborPredicate to determine if a neighbor satisfies conditions.

WalkPredicate(KernelPointCursor, NeighborPredicate, boolean) - Constructor for class WalkPredicate

WalkRunnable - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel

Walks in X, Y and Z directions from a point, executing a Runnable if the neighbor satisfies conditions.

WalkRunnable(KernelPointCursor, Predicate<Point3i>, Runnable) - Constructor for class WalkRunnable

WatershedEncoding - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding

WatershedEncoding() - Constructor for class WatershedEncoding

WatershedYeong - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong

A 'rainfall' watershed algorithm

WatershedYeong() - Constructor for class WatershedYeong

WeightedKernel<T,S> - Class in org.anchoranalysis.mpp.segment.optimization.kernel

A kernel with an associated weight.

WeightedKernel(Kernel<T, S>, double) - Constructor for class WeightedKernel

Constructor for single kernel factory

WeightedKernelList<T,S> - Class in org.anchoranalysis.mpp.segment.optimization.kernel

WeightedKernelList() - Constructor for class WeightedKernelList

weightFor(Mark) - Method in class ConstantWeight

weightFor(Mark) - Method in class ExtractWeightFromMark

weightFor(Mark) - Method in class NumberPoints

weightWidthDescription() - Method in class AnnotatorStrategy

The degree as to how lengthy the labels from AnnotatorStrategy.annotationLabelFor(ProvidesStackInput, Logger) can be.

weightWidthDescription() - Method in class ImageLabelStrategy

weightWidthDescription() - Method in class MarkProposerStrategy

with(Feature<T>, Logger) - Static method in class FeatureSession

Starts a feature-session for a single feature.

with(Feature<T>, SharedFeatures, Logger) - Static method in class FeatureSession

Starts a feature-session for a single feature.

with(Feature<T>, FeatureInitialization, SharedFeatures, Logger) - Static method in class FeatureSession

with(FeatureList<T>, Logger) - Static method in class FeatureSession

Starts a feature-session for a list of features.

with(FeatureList<T>, FeatureInitialization, SharedFeatures, Logger) - Static method in class FeatureSession

with(FeatureList<T>, FeatureInitialization, Optional<SharedFeatures>, Logger, BoundReplaceStrategy<T, ? extends ReplaceStrategy<T>>) - Static method in class FeatureSession

with(BoundingBox) - Method in class BoundingBoxIntersection

Finds the intersection with another bounding-box, if it exists.

with(BoundingBox) - Method in class BoundingBoxUnion

Performs a union with another box (immutably).

withBackgroundAndColors(DrawObject, DisplayStack, ColorIndex) - Static method in class DrawObjectsGenerator

A generator that draws an object in a particular way with particular colors and background.

withBuffer(Mask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class IterateVoxelsMask

Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo

withBuffer(Voxels<T>, ProcessBufferUnary<T>) - Static method in class IterateVoxelsAll

Iterate over each voxel - with one associated buffer for each slice.

withBuffer(BoundingBox, Voxels<T>, ProcessBufferUnary<T>) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box - with one associated buffer for each slice

withBuffer(ObjectMask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.

withBuffer(Optional<ObjectMask>, Voxels<T>, ProcessBufferUnary<T>) - Static method in class IterateVoxelsObjectMaskOptional

Iterate over each voxel (or optionally only on object-mask) with one associated buffer.

withCalculateLevel(Histogram, CalculateLevel) - Static method in class HistogramThresholder

Retains the portion of the histogram greater or equal to the calculated-level

WithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider

WithChannelBase() - Constructor for class WithChannelBase

WithContainerBase - Class in org.anchoranalysis.plugin.image.bean.object.provider

Base class for ObjectCollectionProvider that take an optional objectsContainer bean-field.

WithContainerBase() - Constructor for class WithContainerBase

withCursor(BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateVoxelsAll

Iterate over each voxel using a KernelPointCursor.

withCursor(BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box using a KernelPointCursor.

withCursorUntil(BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box using a KernelPointCursor until a predicate returns true..

WithDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider

Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.

WithDimensionsBase() - Constructor for class WithDimensionsBase

WithFilterBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider

WithFilterBase(int) - Constructor for class WithFilterBase

within(Optional<ObjectMask>, Extent, ProcessVoxelNeighborAbsolute<T>) - Static method in class ProcessVoxelNeighborFactory

Creates to process neighbors that must lie within either an object-mask or an extent (as a fallback).

withinExtent(ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T>) - Static method in class ProcessVoxelNeighborFactory

Creates to process neighbors that must lie within an extent.

withinMask(ObjectMask, ProcessChangedPointAbsoluteMasked<T>) - Static method in class ProcessVoxelNeighborFactory

Creates to process neighbors that must lie within an ObjectMask.

withinMask(ObjectMask, ProcessVoxelNeighborAbsolute<T>) - Static method in class ProcessVoxelNeighborFactory

Creates to process neighbors that must lie within an ObjectMask.

withInputs(List<S>) - Method in class InputsWithDirectory

Changes the inputs, but preserves the directory.

withinRangeValue(double, FeatureCalculationInput<T>) - Method in class CompareWithRange

withinRangeValue(double, FeatureCalculationInput<T>) - Method in class CompareWithRangeFeature

withinRangeValue(double, FeatureCalculationInput<T>) - Method in class IfConditionWithinRange

withinRangeValue(double, FeatureCalculationInput<T>) - Method in class IfOutsideRange

withinRangeValue(double, FeatureCalculationInput<T>) - Method in class RangeCompareBase

What value to return if the value is inside the range

withInside(BoundingBox, Extent) - Method in class BoundingBoxIntersection

Finds the intersection and clamp to a a containing extent.

withLabel(String) - Method in class Divider

Creates a line of repeated dashes with a centered label of text.

withManifestFunction(String) - Static method in class OutputSequenceStackFactory

The stacks that are outputted are guaranteed to be two-dimensional.

withMatchingPoints(BoundingBox, Predicate<Point3i>, ProcessPoint) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box that matches a predicate.

WithOptionalDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider

Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.

WithOptionalDimensionsBase() - Constructor for class WithOptionalDimensionsBase

withoutColor() - Method in class ColoredOverlayCollection

withoutLabel() - Method in class Divider

Creates a line of repeated dashes.

withoutOrder(OutputPatternStringSuffix) - Method in class OutputSequenceFactory

Writes elements (indexed by strings) to directory, without any order in the sequence.

withoutOrderCurrentDirectory(String, OutputterChecked) - Method in class OutputSequenceStackFactory

Creates a sequence of stacks in the current context's directory that has no pattern.

withoutOrderCurrentDirectory(String) - Method in class OutputSequenceFactory

Writes elements (indexed by strings) to the current directory, without any order in the sequence.

withoutOrderSubset(NamedProvider<Stack>, String, boolean, OutputterChecked) - Method in class OutputSequenceStackFactory

Writes all or a subset from a set of named-stacks to a directory.

WithoutOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle

Avoids including an output-name in the filename.

WithoutOutputNameStyle(String) - Constructor for class WithoutOutputNameStyle

withoutParameters() - Method in class EnergyStack

The energy-stack without associated parameters.

withoutProgressReporter() - Method in interface CheckedProgressingSupplier

Converts to a CheckedSupplier which performs the same operation without updating the progress.

withoutProperties() - Method in class ObjectCollectionWithProperties

Returns the contained-objects without the corresponding properties.

withoutThumbnail() - Method in class LabelledResultsVectorWithThumbnail

Exposes as a LabelledResultsVector without a thumbnail.

withPoint(Extent, ProcessPoint) - Static method in class IterateVoxelsAll

Iterate over each voxel in an Extent

withPoint(BoundingBox, ProcessPoint) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box

withPoint(ObjectMask, ProcessPoint) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel that is located on an object-mask

withPoint(ObjectMask, Optional<ObjectMask>, ProcessPoint) - Static method in class IterateVoxelsObjectMask

Iterate over each point that is located on an object-mask AND optionally a second-mask

withPoint(Optional<ObjectMask>, Extent, ProcessPoint) - Static method in class IterateVoxelsObjectMaskOptional

Iterate over all points that are located on a object-mask or else all points in an extent.

withPointAndIndex(Extent, ProcessPointAndIndex) - Static method in class IterateVoxelsAll

Iterate over each voxel in an Extent.

withPointAndIndex(BoundingBox, ProcessPointAndIndex) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box

withProgressReporter(Progress) - Method in class InputManagerParameters

WithRadiusBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider

A ChannelProviderUnary with a 'radius' parameter

WithRadiusBase() - Constructor for class WithRadiusBase

WithResolutionBase<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical

Base-class for a feature that requires input-resolution to be calculated.

WithResolutionBase(Feature<T>) - Constructor for class WithResolutionBase

WithResolutionBase() - Constructor for class WithResolutionBase

withSlidingBuffer(Optional<ObjectMask>, SlidingBuffer<?>, ProcessPoint) - Static method in class IterateVoxelsObjectMaskOptional

Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object

withThreeBuffers(Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class IterateVoxelsAll

Iterate over each voxel - with three associated buffers for each slice.

withThreeBuffers(BoundingBox, ReadableTuple3i, ReadableTuple3i, Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box - with three associated buffers for each slice.

withTwoBuffers(BoundedVoxels<T>, BoundedVoxels<T>, ProcessBufferBinary<T, T>) - Static method in class IterateVoxelsIntersectingBounded

Iterates over the intersection of two bounded-voxels of type BoundedVoxels.

withTwoBuffers(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, ProcessBufferBinary<UnsignedByteBuffer, UnsignedByteBuffer>) - Static method in class IterateVoxelsIntersectingBounded

Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.

withTwoBuffers(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one VoxelBuffer and one Buffer

withTwoBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel with a corresponding on value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e.

withTwoBuffers(Optional<ObjectMask>, Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class IterateVoxelsObjectMaskOptional

Iterate over each voxel (or optionally only on object-mask) with two associated buffers.

withTwoBuffersAndPoint(Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class IterateVoxelsAll

Iterate over each voxel - with two associated buffers for each slice

withTwoBuffersUntil(BoundedVoxels<T>, BoundedVoxels<T>, PredicateBufferBinary<T>) - Static method in class IterateVoxelsIntersectingBounded

Iterates over the intersection of two bounded-voxels of type BoundedVoxels until a predicate is satisfied.

withTwoBuffersUntil(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, PredicateBufferBinary<T>) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.

withTwoBuffersWithoutOffset(VoxelBuffer<S>, VoxelBuffer<T>, ProcessBufferBinaryWithoutOffset<S, T>) - Static method in class IterateVoxelsRemaining

Iterate over remaining voxels each voxel - with two associated buffers for each slice.

withTwoMixedBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinaryMixed<S, T>) - Static method in class IterateVoxelsAll

Iterate over each voxel in a bounding-box - with one associated voxel-buffer and one associated buffer for each slice.

withTwoMixedBuffers(BoundingBox, ReadableTuple3i, Voxels<S>, Voxels<T>, ProcessBufferBinaryMixed<S, T>) - Static method in class IterateVoxelsBoundingBox

Iterate over each voxel in a bounding-box - with two associated buffers for each slice.

withTwoMixedBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessVoxelBufferBinaryMixed<S, T>) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel in an object-mask - with one associated voxel-buffer and one associated buffer for each slice.

withTwoVoxelBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class IterateVoxelsAll

Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice

withTwoVoxelBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel in an object-mask - with two associated voxel-buffers and for each slice.

WithValueBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean

Operations that use a specified constant value

WithValueBase() - Constructor for class WithValueBase

withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class IterateVoxelsAll

Iterate over each voxel - with one associated voxel-buffer for each slice.

withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnaryWithPoint<T, E>) - Static method in class IterateVoxelsAll

Iterate over each voxel - with one associated voxel-buffer for each slice.

withVoxelBuffer(ObjectMask, Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel on an object-mask with one associated VoxelBuffer.

withVoxelBuffer(ObjectMask, Voxels<T>, Optional<BoundingBox>, ProcessVoxelBufferUnary<T>) - Static method in class IterateVoxelsObjectMask

Iterate over each voxel on an object-mask with one associated VoxelBuffer.

WrapAsUpdatable - Class in org.anchoranalysis.plugin.image.object.merge.condition

Wraps a BeforeCondition as an UpdatableBefoerCondition

WrapAsUpdatable(BeforeCondition) - Constructor for class WrapAsUpdatable

wrapDuplicate(List<Feature<T>>) - Static method in class FeatureListFactory

Wraps an existing list, WITHOUT reusing the list in the internals of the FeatureList i.e.

wrapRaw(byte[]) - Static method in class UnsignedByteBuffer

Exposes a raw byte-array as a buffer with unsigned-bytes.

wrapRaw(ByteBuffer) - Static method in class UnsignedByteBuffer

Exposes a raw ByteBuffer as a buffer with unsigned-bytes.

wrapRaw(int[]) - Static method in class UnsignedIntBuffer

Exposes a raw int-array as a buffer with unsigned-ints.

wrapRaw(IntBuffer) - Static method in class UnsignedIntBuffer

Exposes a raw UnsignedIntBuffer as a buffer with unsigned-ints.

wrapRaw(short[]) - Static method in class UnsignedShortBuffer

Exposes a raw short-array as a buffer with unsigned-shorts.

wrapRaw(ShortBuffer) - Static method in class UnsignedShortBuffer

Exposes a raw UnsignedShortBuffer as a buffer with unsigned-shorts.

wrapReuse(List<Feature<T>>) - Static method in class FeatureListFactory

Wraps an existing list, reusing the list in the internals of the FeatureList

WrapStackAsTimeSequenceStore - Class in org.anchoranalysis.image.io.stack.time

WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>) - Constructor for class WrapStackAsTimeSequenceStore

WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>, int) - Constructor for class WrapStackAsTimeSequenceStore

write(T, Path) - Method in interface AnnotationWriter

Saves the annotation to the filesystem.

write(ImageLabelAnnotation, Path) - Method in class ImageLabelAnnotationWriter

write(DualMarksAnnotation<T>, Path) - Method in class DualMarksAnnotationWriter

write(T, OutputNameStyle, ElementOutputter) - Method in class RasterGenerator

write(Collection<T>, OutputNameStyle, ElementOutputter) - Method in class CollectionGenerator

write(T, OutputNameStyle, ElementOutputter) - Method in class CombinedListGenerator

write(Manifest, OutputNameStyle, ElementOutputter) - Method in class ManifestGenerator

write(S, OutputNameStyle, ElementOutputter) - Method in class GeneratorBridge

write(T, OutputNameStyle, ElementOutputter) - Method in class SingleFileTypeGenerator

write(T, OutputNameStyle, ElementOutputter) - Method in class TransformingGeneratorBridge

write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class AlwaysAllowed

write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class CheckIfAllowed

write(T, OutputNameStyle, ElementOutputter) - Method in interface ElementWriter

Writes a non-indexable output (an output that isn't part of a collection of other similar items)

write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface Writer

Writes an element using an ElementWriter to the current directory.

write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class WriterRouterErrors

Writes an element using an ElementWriter to the current directory.

write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes) - Method in class DrawObject

write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class DrawObject

writeAsRGB(Stack) - Method in class StackWriteAttributes

Whether to write a stack in RGB mode?

writeCross(Point3i, RGBColor, RGBStack, int, BoundingBox) - Static method in class Midpoint

writeEnergyStack() - Method in class EnergyStackWriter

writeFeaturesIntoReporter(U, CSVWriter, Optional<String>, Logger) - Method in class ExportReportFeatures

writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class FeatureListCSVGeneratorHorizontal

writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class FeatureListCSVGeneratorVertical

writeFeaturesToCSV(CSVWriter, T, List<String>) - Method in class FeatureTableCSVGenerator

Writes the features to the CSV-file.

writeFeaturesToCSV(CSVWriter, List<ImageAnnotation>, List<String>) - Method in class AnnotationAggregateCSVGenerator

writeFileToOperationRecorder(String, Path, ManifestDescription, String) - Method in class OutputterChecked

Writes a file-entry to the operation recorder

writeFileToOperationRecorder(String, Path, ManifestDescription, String) - Method in class ElementOutputter

Writes a file-entry to the operation recorder

writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterCreator>, InputOutputContext) - Method in class FeatureResultsAndThumbnails

Writes all the results that have been collected as a CSV file.

writeGroupOutputInSubdirectory(String, T, ConsistentChannelChecker, InputOutputContext) - Method in class GroupMapByName

writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, FeatureOutputMetadata, FeatureCSVWriterCreator, InputOutputContextSubdirectoryCache) - Method in class GroupedResults

Writes outputs for groups that have been previously added with GroupedResults.addResultsFor(org.anchoranalysis.feature.io.results.LabelledResultsVector).

writeHeaders(List<String>) - Method in class CSVWriter

writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class LevelPerObjectBase

Creates a channel with the levels for a set of objects

writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class LevelPerObjectIndependently

writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class LevelPerObjectNeighbors

writeOffByte(int, UnsignedByteBuffer) - Method in class SliceThresholder

WriteOperationRecorder - Interface in org.anchoranalysis.io.manifest.operationrecorder

Makes a record of an output written to the filesystem.

writeOverlays(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>) - Method in class DrawOverlay

Writes a collection of colored-overlays to the background

writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class SimpleOverlayWriter

writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class DrawOverlay

writePrecalculatedMask(RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class PrecalculationOverlay

writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class SimpleOverlayWriter

writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class DrawOverlay

Write precalculated overlays onto the RGBStack.

writer(OutputWriteSettings) - Static method in class GeneratorOutputter

Gets the default StackWriter.

Writer - Interface in org.anchoranalysis.io.output.writer

Write data via ElementWriters to the file system, or creates new sub-directories for writing data to.

writeRaster(FileSaver, String, boolean) - Method in class ImageJRasterWriter

Writes an annotation to the filesystem at outPath.

writeRaster(FileSaver, String, boolean) - Method in class PNG

writeRaster(FileSaver, String, boolean) - Method in class Tiff

writeRelPoint(Point3i, RGBColor, RGBStack, BoundingBox) - Static method in class Midpoint

WriterErrorMessageHelper - Class in org.anchoranalysis.image.io.bean.stack.writer

Helps create similar error messages among StackWriters.

WriteResolutionXml - Class in org.anchoranalysis.plugin.io.bean.stack.writer

When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.

WriteResolutionXml() - Constructor for class WriteResolutionXml

writeResolutionXml(Resolution, Path) - Static method in class ResolutionAsXml

Writes a XML metadata file describing the image-resolution.

WriterExecuteBeforeEveryOperation - Interface in org.anchoranalysis.io.output.writer

writerMultiplex(boolean) - Method in class Outputter

Multiplexes between the selective and permissive writers based on a flag.

writeRow(List<TypedValue>) - Method in class CSVWriter

writeRow(String, String) - Method in class SharedStateFilteredImageOutput

writeRow(String, int, double) - Method in class SharedStateSelectedSlice

writerPermissive() - Method in class Outputter

The writer that allows all outputs.

WriterRouterErrors - Class in org.anchoranalysis.io.output.writer

Write data via ElementWriters to the file system, or creates new sub-directories for writng data to.

WriterRouterErrors(Writer, ErrorReporter) - Constructor for class WriterRouterErrors

writers() - Method in interface OutputSequence

writers() - Method in class OutputSequenceIncrementing

writers() - Method in class OutputSequenceIndexed

writerSecondLevel(String) - Method in class Outputter

A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.

writerSelective() - Method in class Outputter

The writer that allows only certain selected outputs.

writeSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class DrawObject

Draws a single-object on top of a RGB-stack

writeStack(Stack, Path, StackWriteOptions) - Method in class OneOrThreeChannelsWriter

writeStack(Stack, Path, StackWriteOptions) - Method in class StackWriter

Writes a stack to the filesystem at a particular path.

writeStack(Stack, Path, StackWriteOptions) - Method in class BioformatsWriter

writeStack(Stack, Path, StackWriteOptions) - Method in class Tiff

writeStack(Stack, Path, StackWriteOptions) - Method in class ImageJRasterWriter

writeStack(Stack, Path, StackWriteOptions) - Method in class StackWriterDelegateBase

writeStack(Stack, Path, StackWriteOptions) - Method in class WriteResolutionXml

writeStackAfterCheck(Stack, Path) - Method in class OneOrThreeChannelsWriter

writeStackAfterCheck(Stack, Path) - Method in class ImageIOWriter

writeStackAfterCheck(Stack, Path) - Method in class OpenCVWriter

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class OneOrThreeChannelsWriter

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class StackWriter

Writes a series of stacks to the filesystem at a particular path.

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class BioformatsWriter

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class NoTimeSeries

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class SupportsTimeSeries

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class StackWriterDelegateBase

writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class WriteResolutionXml

writeStackTime(Stack, Path, boolean) - Method in class ImageJRasterWriter

Writes a stack as a time-sequence (many images together in a single file.).

writeStackWithExtension(Stack, Path, StackWriteOptions) - Method in class StackWriter

Writes a stack to the filesystem at a particular path with an extension appended to the path.

WriteStringToFile - Class in org.anchoranalysis.io.generator.text

writeThresholdedByte(int, UnsignedByteBuffer, VoxelBuffer<?>, VoxelBuffer<?>) - Method in class SliceThresholder

writeToFile(Path) - Method in class Dictionary

Serializes the key-value parameters to a file.

writeToFile(T, OutputWriteSettings, Path) - Method in class FeatureTableCSVGenerator

writeToFile(Histogram, OutputWriteSettings, Path) - Method in class HistogramCSVGenerator

writeToFile(ObjectCollection, OutputWriteSettings, Path) - Method in class HDF5ObjectsGenerator

writeToFile(T, Stack, StackWriteOptions, OutputWriteSettings, Path) - Method in class RasterGenerator

Writes a raster to the file-system.

writeToFile(T, Stack, StackWriteOptions, OutputWriteSettings, Path) - Method in class RasterGeneratorSelectFormat

writeToFile(StackSeries, OutputWriteSettings, Path) - Method in class RGBTimeSeriesGenerator

writeToFile(Dictionary, OutputWriteSettings, Path) - Method in class DictionaryGenerator

writeToFile(T, OutputWriteSettings, Path) - Method in class ObjectOutputStreamGenerator

writeToFile(T, OutputWriteSettings, Path) - Method in class XStreamGenerator

writeToFile(T, OutputWriteSettings, Path) - Method in class SingleFileTypeGenerator

writeToFile(T, OutputWriteSettings, Path) - Method in class SingleFileTypeGeneratorBridge

writeToFile(String, OutputWriteSettings, Path) - Method in class StringGenerator

writeToXML(CSVRow, Element, Document) - Method in class ColumnDefinition

writeToXML(CSVRow, Element, Document) - Method in class Pairwise

writeToXML(CSVRow, Element, Document) - Method in class Single

writeToXML(Element, Document) - Method in class CSVRow

writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class RasterGenerator

As only a single-file is involved, this methods delegates to a simpler virtual method.

writeWithIndex(Collection<T>, String, IndexableOutputNameStyle, ElementOutputter) - Method in class CollectionGenerator

writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class CombinedListGenerator

writeWithIndex(Manifest, String, IndexableOutputNameStyle, ElementOutputter) - Method in class ManifestGenerator

writeWithIndex(S, String, IndexableOutputNameStyle, ElementOutputter) - Method in class GeneratorBridge

writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class SingleFileTypeGenerator

writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class TransformingGeneratorBridge

writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class AlwaysAllowed

writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class CheckIfAllowed

writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in interface ElementWriter

Writes an indexable output (many outputs of the same type, uniquely identified by an index)

writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in interface Writer

Writes an indexed-element using an ElementWriter in the current directory.

writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class WriterRouterErrors

Writes an indexed-element using an ElementWriter in the current directory.

writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class AlwaysAllowed

writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class CheckIfAllowed

writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface Writer

Writes an element using an ElementWriter to the current directory, without including an output name in the path.

writeXmlToFile(Document, Path) - Static method in class XMLWriter

Writes a XML-document to the file-system.

X

x() - Method in class Dimensions

The size in the X dimension.

x() - Method in class Resolution

The resolution in the X-dimension in meters.

x(int) - Method in class BoundingBoxContains

Is this value in the X-dimension within the bounding box range?

x() - Method in class Extent

The size in the X dimension.

x() - Method in class DirectionVector

The x-component of the vector.

x() - Method in class Point2d

X-axis component of point.

x() - Method in class Point2f

X-axis component of point.

x() - Method in class Point2i

X-axis component of point.

x() - Method in interface ReadableTuple3i

X-axis component of the tuple.

x - Variable in class Tuple3d

X-axis component of the tuple.

x() - Method in class Tuple3d

X-axis component of the tuple.

x - Variable in class Tuple3f

X-axis component of the tuple.

x() - Method in class Tuple3f

X-axis component of the tuple.

x(float) - Method in class Tuple3f

X-axis component of the tuple.

x - Variable in class Tuple3i

X-axis component of the tuple.

x() - Method in class Tuple3i

x() - Method in class ScaleFactor

How much to multiply the existing x-dimension by to create a scaled X-dimension.

xFromChainCode(int) - Static method in class ChainCodesDirection

XMLGenerator<T> - Class in org.anchoranalysis.io.generator.xml

XMLGenerator() - Constructor for class XMLGenerator

XMLParser - Class in org.anchoranalysis.core.serialize

Utility functions for parsing XML files using standard Java APIs.

XMLWriter - Class in org.anchoranalysis.io.output.xml

Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine

Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.

Xor() - Constructor for class Xor

XStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize

Deserializes an object using the XStream library.

XStreamDeserializer() - Constructor for class XStreamDeserializer

XStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized

XStreamGenerator() - Constructor for class XStreamGenerator

XStreamGenerator(Optional<String>) - Constructor for class XStreamGenerator

XStreamSerializer - Class in org.anchoranalysis.core.serialize

Serializes an object using the XStream library.

XYOrientationExtendToZ - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points

XYOrientationExtendToZ() - Constructor for class XYOrientationExtendToZ

Y

y() - Method in class Dimensions

The size in the Y dimension.

y() - Method in class Resolution

The resolution in the Y-dimension in meters.

y(int) - Method in class BoundingBoxContains

Is this value in the Y-dimension within the bounding box range?

y() - Method in class Extent

The size in the Y dimension.

y() - Method in class DirectionVector

The y-component of the vector.

y() - Method in class Point2d

Y-axis component of point.

y() - Method in class Point2f

Y-axis component of point.

y() - Method in class Point2i

Y-axis component of point.

y() - Method in interface ReadableTuple3i

Y-axis component of the tuple.

y - Variable in class Tuple3d

Y-axis component of the tuple.

y() - Method in class Tuple3d

Y-axis component of the tuple.

y - Variable in class Tuple3f

Y-axis component of the tuple.

y() - Method in class Tuple3f

Y-axis component of the tuple.

y(float) - Method in class Tuple3f

Y-axis component of the tuple.

y - Variable in class Tuple3i

Y-axis component of the tuple.

y() - Method in class Tuple3i

y() - Method in class ScaleFactor

How much to multiply the existing y-dimension by to create a scaled Y-dimension.

yFromChainCode(int) - Static method in class ChainCodesDirection

Z

z() - Method in class Dimensions

The size in the Z dimension.

z() - Method in class Resolution

The resolution in the Z-dimension in meters.

z(int) - Method in class BoundingBoxContains

Is this value in the Z-dimension within the bounding box range?

z() - Method in class Extent

The size in the Z dimension.

z() - Method in class DirectionVector

The z-component of the vector.

z() - Method in interface ReadableTuple3i

Z-axis component of the tuple.

z - Variable in class Tuple3d

Z-axis component of the tuple.

z() - Method in class Tuple3d

Z-axis component of the tuple.

z - Variable in class Tuple3f

Z-axis component of the tuple.

z() - Method in class Tuple3f

Z-axis component of the tuple.

z(float) - Method in class Tuple3f

Z-axis component of the tuple.

z - Variable in class Tuple3i

Z-axis component of the tuple.

z() - Method in class Tuple3i

zChange - Variable in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer

The change in the Z-dimension to reach this neighbor relative to the source coordinate.

ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask

Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.

ZeroOutsideMask() - Constructor for class ZeroOutsideMask

zeroValue(int) - Method in class Histogram

Sets the count for a particular value to 0.

zFromChainCode(int) - Static method in class ChainCodesDirection

zIfDefined(double) - Method in class Resolution

Returns the z-resolution like Resolution.z() if the z-resolution is not Double.NaN.

zip(Collection<S>, Collection<T>) - Static method in class FunctionalList

Create a list of pairs of elements from two separate collections.

zRelative() - Method in class Resolution

Gives the relative resolution of the z-component to the x-component.

zScore(double) - Method in class MeanScale

Converts a value to a z-score given the parameterization in this object.

ZScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics

ZScore() - Constructor for class ZScore

ZScoreCalculator - Class in org.anchoranalysis.math.statistics

Calculates a Z-Score.

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